MAExplorer - Microarray Exploratory Data Analysis

4. Status and Bugs of MAExplorer

This section discusses the status and known bugs in MAExplorer. It also discusses dealing with the reporting of fatal errors so we can resolve them.

Section 4.1 discusses known bugs, Section 4.2 lists the revision notes for older versions known bugs. If you have experienced bugs with an older version of MAExplorer, you might check the revision notes to see if the bug was fixed and download a new version. Section 4.3 discusses problems in using MAExplorer as an applet with Web browsers. Section 4.4 describes handling fatal "DRYROT" errors.

4.1 Known Bugs in MAExplorer

Disclaimer: none of our code ever has bugs... :-). So despite this, we are working on resolving these bugs and implementing planned functionality. Here is a short non-inclusive list of known problems that we are resolving. We welcome and encourage you to E-mail us with any bugs that you find do exist as well as suggestions for capabilities you would like to see. As the new open-source MAEPlugins facility evolves, most new (and some old) functionality will migrate to these plugins. Then the user community can help maintain these analytic methods.

If you encounter a fatal error that is detected by MAExplorer, it will popup an error reporting window. Please E-mail this data to us so we can try to resolve the problem.

In the mean time, partially implemented commands are disabled to keep you out of trouble :-) ...

You can help us and get MAExplorer to do more of the things you would like to see. Let us know of problems that you encounter as well as suggestions for changes or new methods you would like to see - send us E-mail.

4.1.1 Browser Applet Bugs

4.1.2 Downloading and Installer Bugs

4.1.3 Computation speed and display Bugs

4.1.4 User state and login Status

4.1.5 Data file names Bug

4.1.6 Gene Sets Bugs

4.1.7 Clustering Bugs

4.1.9 Expression profile Bugs

4.1.9 Data conversion problems

4.1.10 Java Plugins Bugs

4.1.1 Browser Applet Bugs

When using MAExplorer as a Web browser applet (this does not apply if running as a stand-alone application - and we recommend running it as a stand-alone application not as an applet), there are problems with running MAExplorer on some of the Web browsers on some operating systems. It generally works with Netscape 4.7 or later, on Windows PCs (95/98/NT/2000/XP), and on SUN Unix and with Microsoft Internet Explorer 5.0 on PCs. It may not work as well as an applet on Macintoshes - even with Internet Explorer (although it works fine as a stand-alone application on the Mac) and problems have been reported on SGI systems because of browser problems.
If you are experiencing Web browser problems using the MAExplorer applet, you might check the discussion of possible solutions.
When run as a Web browser applet, you should only click once since multiple clicks may cause some browsers to hang. Note that when you click the first time, it starts downloading the applet. Clicking a second time may cause a second request for the applet to be launched. This interferes with the first request and so neither is started correctly.
When the MAExplorer applet is being downloaded, some browsers do not indicate to the user that it is being downloaded and so it may appear that nothing is going on. Some browsers will not indicate that it is downloading an applet. So please be patient. When it starts, the main window will popup and it continues to download data. Wait a while for it to load the applet before giving up. For a 28Kb Internet connection, this could take several minutes. When it is finished, the menu bar will become active and it will display Ready - click on a gene to query database.

4.1.3 Downloading and Installer Bugs

We have had reports of problems with MAExplorer installations or running MAExplroer on MacOS 9 since we started distributing MAExplorer with the new InstallAnywhere version 5.0.2. We suggest you switch to MacOS-X or use a Windows, Linux or Solaris system until this gets resolved.
Installer does not start or does not download the data. Normally, when you attempt to download MAExplorer to your computer, the InstallAnywhere software running in your Web browser will detect which OS you are running and suggest the particular download to use in:
```
     "Recommended version for your computer
      Download installer for ...your OS..."?
```
Occasionally, we have seen instances where you can not install MAExplorer from within the Web browser. The solution is to explicitly download the particular Platform for your OS in the Available Installers list. And then to follow the instructions on running it.
If you have problems downloading this with Netscape 4.7x or later, then try Internet Explorer 5.0. It could be a Mime/type problem with your particular browser not setup correctly.
On Solaris, and possibly other Unix systems, you may have problems with the stack limits. Do a "man limit" to read about the command for your particular Unix shell. We have found that the following seems to work. For CSH, add the following to your .cshrc startup file. With versions 96.25 and later of MAExplorer, you may adjust the memory size using the (Edit menu | Preferences | Resize MAExplorer memory limits for the next time it is run) command. This edits the startup file according to the new memory limits you specify.
```
   limit stacksize unlimited
```

4.1.4 Computation speed and display Bugs

Because it does a lot of computation, MAExplorer runs best on a fast computer with lots of memory. An optimal system should have at least 128Mb of memory at least 500Mhz CPU speed. For doing hierarchical clustering we recommend 256Mb of memory which will allow you to cluster larger sets of genes without paging the operating system. So you may run into problems with running out of memory on an under-powered computer. To increase the usable memory size to more than 256Mb (assuming your computer has it), then you may need to edit the MAExplorer.lax file that resides where you installed MAExplorer on your computer to increase the heap and stack maximum limit.
We have seen instances where the same system will run out of memory with particular Web browsers (again - not a problem when running stand-alone) Netscape 4.7 on a system with a lot of memory. This does not seem to happen with Internet Explorer 5.0. This is because Netscape4.7 on the Windows PC seems to be able to use only about 5.5Mb before it runs out of memory. This is not the case with Internet Explorer 5.0.
MAExplorer is difficult to use with a system with a small screen because of the size and number of multiple graphic images and plots. We recommend a screen size of at least 1024x768. As they say these days, more is better :-), generally.
For problems with MAExplorer and MacOS, you might also see our MacOS problems FAQ.
For problems with MAExplorer and Sun Solaris OS, you might also see our SUNOS problems FAQ.
We have on rare occasions seen a data-related problem on MacOS systems. If the data was edited in such a way that the line terminators were Return characters instead of Linefeeds or Return-Linefeeds, the data may become corrupted and MAExplorer has difficulty reading it. The solution is to replace the Return characters with Linefeeds or Return-Linefeeds. One (painful) way this might be done by exporting the data to a system such as a Windows PC; read the data into Excel; save it as an Excel worksheet file format; exit Excel; start Excel again on the new data files; save the data files back into the original MAExplorer directories as tab-delimited text files. MAExplorer should recognize Return as the line terminator. This bug will be resolved in a future release.

4.1.5 User state and login Status

User registration and the groupware access functionality are not available yet. However, login is available for collaborator databases on the MGAP MAExlorer Web server.
The commands to save and restore user states for a particular user on the back-end server are not available yet. However, in stand-alone mode you may save the state (including all gene and condition sets, parameter conditions, condition sets, etc) on a local computer by doing a (File menu | Databases | Save As DB). The specialized groupware commands that will allow users to selectively share their saved states with particular other users on a public groupware server is not available yet.

4.1.6 Data file names Bug

There is a potential problem with using long file names when using MAExplorer with MacOS-8 or MacOS-9. Both of these operating systems limit file names to 32 characters. This could be a problem if importing data from another operating system (Windows, Unix, Linux, etc) that does not have this restriction. The solution is to use short file names. This should not be a problem with MacOS-X since it allows file names with up to 256 characters.

4.1.7 Gene Sets Bugs

The full range of GeneClass subsets (Section 2.4.1) is not available yet. However, you may use the gene name guesser to find a set of genes by wildcard into the Edited Gene List (e.g. "*ONCO*" to find all oncogenes or proto-oncogenes, etc). These EGL sets may then be saved as named gene sets and used in the data filter as "Filter by 'User Gene Set'". See the Gene Class ontologies using Gene Set operations (Section 2.4.1) that can achieve a similar effect.

4.1.8 Clustering Bugs

The hierarchical clustering method is buggy. It currently clusters genes - but not samples. The latter is under construction. Centroid averaging is implemented and the arithmetic averaging is under construction. Although it generates a clustergram plot, the dendrogram drawing may not be drawn correctly using centroid averaging. Depending on the number of samples, it you do a complete hierarchical cluster for all genes and ESTs on a Netscape browser on a Windows PC, the browser may run out of memory and nothing appears. [When done in the stand-alone application, this is less of a problem since there are no memory restrictions.] You can do three things at this point: 1) switch to Internet Explorer, or 2) decrease the number of genes being clustered (e.g. just "All named genes") or the CV filter. The third option is to disable the clustering cache. This will be done automatically for you and it will continue doing the clustering. You may turn off (or on) the Use cluster distance matrix cache in the "Hierarchical Cluster Plots submenu. It will perform the clustering, but will take MUCH longer without the cache.
If you are working with very large data sets then if you start a find similar genes or K-Means clustering with a very high threshold, you can not change the threshold until it is done. In these situations, try pre-setting the threshold distance, number of clusters using the (Edit | Preferences | Adjust all Filter threshold scrollers). This will popup the state scroller window with all of the thresholds. You may also select the current gene prior to starting clustering.

4.1.9 Expression profile plots

The Expression Profile Overlay display is being improved to offer better graphics and interaction.
We have observed some instances of the popup EP plot where data does not seem to correspond to the data. This may be related to the normalization method.
When viewing an ordered list of EP plots associated with a sorted list of genes (e.g. clustering genes similar to a seed gene), if there are replicated genes in the clustered genes, they may not show up in the scrollable list of EP plots.

4.1.10 Data conversion problems

The Cvt2Mae data file converter application is currently available for beta-testing on the a related MAExplorer Cvt2Mae Web page. It enables users to convert their data files (academic one-of-a-kind as well as commercial e.g. Affymetrix, Incyte, GenePix, Scanalyze, etc) to the standard MAExplorer files as described in Appendix C and D.
If you are not able to convert your data using Cvt2Mae (which is currently in early Beta testing - see the Cvt2Mae Web page for current status), you can always manually convert the data using the examples in Appendix C.
We have seen some problems running the converter with some types of data on MacOS 8-9. The temporary solution is to convert your data using another system such as Windows until we fix the problem.
If you are using the NCI-CIT mAdb system to package data for MAExplorer, you must select all samples from multiple projects that you want to compare with MAExplorer while packing the data in mAdb. (See PDF document "How to download mAdb data For MAExplorer") Currently, you can not easily merge the data after you have downloaded the files to your computer. The solution is to use mAdb to prepackage all data you want to analyze in a single .zip file. You can not currently merge data from separately unzipped files (without manually editing the SamplesDB.txt file). The way you package data using mAdb is to: 1) select ALL of the projects that contain samples that you want (on the mAdb "Top Level Analysis Selection" web page); 2) further select the exact subset of samples that you want in the "Array Selection" table on the "mAdb: Database Retrieval" web page). NOTE: currently, you can only select arrays using the same GAL file so they have compatible geometries. This is on our list of things to change so you can mix and match data from different chips.

4.1.11 Java Plugins bugs

Java Plugins are in the process of being implemented and will be made available to the user community to enable them to add their own analysis methods to MAExplorer.

4.2 Revision notes

This section lists the revision history and is useful for deciding whether to upgrade to the most recent release. You may want to check for the latest the current "Stable release" available on the MAExplorer Web site. That may be different than the Stable release listed in this copy of the Reference Manual. The "Beta release" listed below the Stable release in the previous links is experimental and may generally be downloaded as it has more functionality. If you experience problems, you can just reinstall the Stable version.

Note: An archive of some of the stable older releases is available on the NCI/LECB Web site for a limited period.

Version 0.96.34.01: (11-24-2003) Fixed problem introduced in the previous release where you could not increase the memory size invoked by the (Edit | Preferences | Resize MAExplorer memory limits for the next time it is run) command. To fix this bug you must reinstall MAExplorer using the full download using the Java installers. Also added ability to visualize the CV (coefficient of variation of a set of replicate samples) using the new (Analysis | Plots | Show microarray | Pseudocolor HP-EP 'list' CV (Coefficient of Variation) [RB]) command. It computes the CV for the HP list. So use the (Samples | Choose HP-X, HP-Y and HP-E samples) command to define the HP-EP list of samples you want to investigate.
Version 0.96.33.07: (08-15-2003) The code implementing the R eval paragigm has been refactord so that it is clearer and will be easier to use for other projects. See the RtestPlugin documentation Section 6 for details.
Version 0.96.33.04: (07-31-2003) Fixed minor bugs in MAExplorer and Reval data export for RLO methods.
Version 0.96.33.03: (07-23-2003) Fixed minor bugs in current OCL state as well as adding support for future MAERlibr.zip updates from the Web.
Version 0.96.33.01: (07-09-2003) Fixed bugs where the XY scatterplot and other functions may not work with some data where there were empty genes in the database. Changed the underlying control mechanism to switch between the 4 clustering methods so it is more robust and easier to use.
Version 0.96.32.10: (06-30-2003) added loessPlot() R method to MAERlibr R library. This is used by RtestPlugin for generated code.
Version 0.96.32.09: (06-26-2003) added new command (Plugin menu | Save RLO reports in time-stamped Report/ folder [CB]). put files generated by R from successive executions of the same RLO into separate sub-folders in the Report/ folder with names "RLOname-YYMMDD-HHMMSS/" to peep the data separate. This is useful when you want to compare results from the same RLO method but with different MAExplorer preprocessing. Also added new command (Analysis menu | Filter | Filter by genes with non-zero intensity) which can be used to omit genes with zero intensity values in any samples of the HP-EP set of samples. This is useful when exporting data to RLOs that may have problems by dividing by 0.0 etc.
Version 0.96.32.08: (06-17-2003) fixed bug in RtestPlugin for Version 0.96.32.07 where it did not always use the intput file mode correctly. Simplied the "Add Template" usage to "Generate Template for 1st input file". Finished inplementing the (Files | Update RLO methods from Web server) so that it updates the MAERlibr package library file (lib/MAERlibr/R/MAERlibr) as well as the .R and .rlo files for the RLO methods.
Version 0.96.32.07: (06-15-2003) fixed RtestPlugin editor bug that did not always setup parameters for New RLO correctly. There is still a but that may require you to set the input files mode to the corresponding Demo BEFORE doing "Add Template". This will be corrected shortly.
Version 0.96.32.06: (06-13-2003) fixed RtestPlugin editor bug that did not always save the Routput files types. Also fixed bug in demo R script Test.R.
Version 0.96.32.05: (06-12-2003) fixed code generators and changed all R methods in the MAExplorer MAERlibr to have a "mae." prefix to minimize conflict with other packages. Added alpha-level support for XY overlay plots in MJAplot class of the API.
Version 0.96.32.04: (06-11-2003) fixed code generators on Demos 1-15. Demos 16-17 now broken with VSTACK error. Major code generators cleanup in RtestPlugin. Demo 15 (with use Filter Action) works but does not toggle the (Analysis | Filter | Filter by user gene set) menu checkbox. Also added code to R2MAE actions to better support reimporting gene sets back into MAExplorer.
Version 0.96.32.03: (06-08-2003) Moved the MAExplorer-R interface R library code from the .R files to an full R library that now is downloaded when you do the full download/install of MAExplorer. We will be adding an update for this MAERlibr library. The Web update is not available currently available.
Version 0.96.32.01: (05-29-2003) Added (Files | Update RLO methods from maexplorer.sourceforge.net) command to update RLO methods from the server. RLO methods consist of pairs of R scripts and RLO files. Note: R must be installed on your computer to use these methods. When MAExplorer is restarted these new RLO methods will be available in the (Plugins | RLO methods) submenu.
Version 0.96.31.23: (05-27-2003) Fixed bug in reading RLOs if they were manually edited with a Windows text editor that replace line feeds with carriage returns.
Version 0.96.31.22: (05-22-2003) Minor changes in RtestPlugin and R evaluation support code.
Version 0.96.31.21: (05-18-2003) Reorganized RtestPlugin code and updated some of the code generators.
Version 0.96.31.20: (05-14-2003) Fixed bug where MAExplorer could crash if R was not installed. This was also in the RtestPlugin. Now, it detects that it is not there if you cancel the prompt for specifying R is when it can't find it. This is noted in a special .RbasePath file which contains "**NO_R_INSTALLED**". This is then used to prevent you trying to access any R commands or menus (i.e. keep you out of trouble).
Version 0.96.31.19: (05-14-2003) Fixed minor bugs in RtestPlugin and support for horizontal and vertical stacked data.
Version 0.96.31.18: (05-08-2003) Fixed minor bugs in RtestPlugin and support.
Version 0.96.31.17: (05-06-2003) Fixed prompt in "Update Plugins".
Version 0.96.31.16: (05-05-2003) Changed the "Update MAEPlugins from maexplorer.sourceforge.net" so that it will download ALL of the plugins if you answer YES rather than one at a time. More cleanup for RtestPlugin Template paradigm.
Version 0.96.31.15: (05-05-2003) In RtestPlugin, simplified R code to use new multi-line header data file paradigm and started to add data model Template generation code. OCL demo does not work with new paradigm.
Version 0.96.31.14: (04-30-2003) Fixed problem with R script evaluation if the sample names had spaces in the name. Quoting these fixed the problem.
Version 0.96.31.12: (04-28-2003) Fixed fatal error problem introduced in 0.96.31.12 if start MAExplorer with no database. This version fixes bugs in some of the RtestPlugin Demo R code generators and data files.
Version 0.96.31.11: (04-25-2003) Fixed quote problem with with executing R in some cases for RtestPlugin. Fixed Prev/Next problem.
Version 0.96.31.10: (04-23-2003) Added "Save ALL Demo RLOs" to RtestPlugin to generated demo RLOs for (Plugins | RLO methods) menu next time MAExplorer is restarted. The demo R Code generators are not validated yet.
Version 0.96.31.9: (04-22-2003) Fixed RtestPlugin problem with sample set names when generate RLOs for XY sets and OCL condition sample sets. Changed the export data formats so easier to use in R. The demo R Code generators are not validated yet.
Version 0.96.31.8: (04-21-2003) Fixed problem with RtestPlugin that sometimes showed up when installed in "C:/Program Files/" on a Windows system (needed to quote the path). It now works on windows. Note: RtestPlugin Demos 10-13 and Demo 16 are not working correctly. The demo R Code generators are not validated yet.
Version 0.96.31.7: (04-18-2003) Gene Set actions now work for RLOs. The demo R Code generators are not validated yet.
Version 0.96.31.5: (04-13-2003) Extended the RLO definition and support code. Extended RtestPlugin to access this. The demo R Code generators are not validated yet.
Version 0.96.31.4: (04-11-2003) Added "RLO methods to Plugins menu. This uses RLO files generated by the RtestPlugin. Additional bug fixes and better error reporting of R evaluation errors. The demo R Code generators are not validated yet.
Version 0.96.31.2: (04-07-2003) Extended RtestPlugin and corresponding changes in MJA API. The demo R Code generators are not validated yet.
Version 0.96.31.1: (04-03-2003) Cleaned up gene filter processing model.
Version 0.96.30.10: (03-29-2003) Better support for RtestPlugin.
Version 0.96.30.8: (03-28-2003) Modified the MJAReval, MJAgeneList, MJAfilter API class methods to support the RtestPlugin. RtestPlugin now supports "New RLO" at alpha level.
Version 0.96.30.6: (03-25-2003) The RtestPlugin editor is working (alpha level) for demonstration purposes-only at this time.
Version 0.96.30.5: (03-18-2003) The RtestPlugin is alpha level. Modified the MJAReval class methods to support this. This is still alpha-level, and may change.
Version 0.96.30.4: (03-17-2003) Added new functionality to evaluate MAExplorer data using the R system. There is a new MJAReval to access methods to do this. Using MJAReval, one can write MAEPlugins to process MAExplorer data in R and to bring back the results into MAExplorer. This is still alpha-level, and may change.
Version 0.96.30.3: (03-04-2003) Fixed radio-button usage of NormalizationPlugin so that only one normalization (either built-in or plugin) is active at a time. The MJA API was enhanced to add this functionality.
Version 0.96.30.2: (03-02-2003) Major ehnancements of the NormalizationPlugin paradigm in the MJA library to support a wide variety of normalization methods - both global and local. This includes support code throughout MAExplorer to support it and to make it easier to debug. Although it works, the NormalizationPlugin is still Alpha-level and will be documented fully when it enters Beta-level code.
Version 0.96.29.3: (02-25-2003) Rebuilt installers (Windows, Linux, Solaris) with Java Virtual Machine (JDK) 1.4.1_01 that has improved performance. You must do a download and reinstall -- not just an update from (File menu | Update MAExplorer from maexplorer.sourceforge.net).
Version 0.96.29.3: (02-23-2003) Added more support for FilterPlugins. The ExampleXYdataFilterPlugin example now works. It is meant to be a model for more sophisticated plugins. [TODO] it needs parameters GUI popdown.
Version 0.96.29.2: (02-21-2003) Fixed many problems with MJA classes where some methods which should have been public were not so MAEPlugins could not access them. This has been corrected. The FtestNconditionsFilterPlugin is now working.
Version 0.96.29.1: (02-19-2003) Added popup alert message window for bettering informing users of conditions that prevent them from doing the operation they requrested. They must press the Close button to pop-down the message, although they can do a SaveAs to a file to save the message. For complex problems, some of the messages may suggest what they need to do to correct the problem.
Version 0.96.28.3: (02-18-2003) Added 2 new filters: "Filter by HP-X,HP-Y 'sets' t-Test [p-Value] slider [RB]" and "Filter by current Ordered Cond. List (OCL) F-Test [p-Value] slider [RB]". The p-Value related Filter tests were changed to radio buttons [RB] so that only one would be operative at a time. If another p-Value dependent test is on, it will be shut off it you select a different p-Value dependent test. Added new support methods in the MJA API in classes MJAsampleList, MJAstatistics, MJAfilter, and MJAmath. Implemented the "List OCL" and "List All" OCLs in the OCL chooser. Improved the GUI legends in the Condition Chooser and the Ordered Condition Chooser.
Version 0.96.28.1: (02-15-2003) fixed default R2 and CR2. Modified State Scrollers paradigm so that it uses slider usage counters (instead of flags) so that MAEPlugins may share sliders (e.g., p-Value, cluster distance, etc).
Version 0.96.27.1: (02-12-2003) added named Ordered Condition List (OCL) editor as a builting method.
Version 0.96.26.1: (02-08-2003) added methods to MJAsampleList to get either normalized Filtered data or normalized complete set of genes data. Fixed bug in CompositeDatabase.
Version 0.96.25.5: (01-28-2003) Fixed bug in "Remove Parameter" in the condition chooser. Added new methods MJAcondition, added method in MJAsampleList to get all raw sample data.
Version 0.96.25.4: (01-13-2003) Fixed bug in "Remove Parameter" in the condition chooser.
Version 0.96.25.3: (01-02-2003) Fixed bug in "Remove Condition" where it previously deleted the wrong condition list.
Version 0.96.25.2: (12-14-2002) Added "Remove Condition" to (Sample menu | Choose named condition lists of samples) as well as fixed several bugs related to the condition chooser. Also added the same command to the (Edit menu | Sets of conditions | Choose named condition lists of samples) menu since it is a condition editing function.
Version 0.96.25.1: (12-11-2002) Made some of the tests for names case-independent for smoother operation.
Version 0.96.25: (12-06-2002) Added new a new command (Sample menu | Choose named condition lists of samples) lets you define or edit new named lists of hybridized samples.
Version 0.96.24.12: (12-04-2002) Added support for RefSeqID and alternate spellings of other genomic identifiers. Modified MAJcondition class to support ConditionChooser.
Version 0.96.24.11: (12-02-2002) Added support for RefSeqID and alternate spellings of other genomic identifiers. Modified MAJcondition class to support ConditionChooser.
Version 0.96.24.10: (11-30-2002) Updated the default URLs used for GenBank, UniGene, LocusLink, and added OMIM ID support.
Cvt2Mae Version 0.73 (11-26-2002) Added ability specify multiple chips/sample (e.g. Affy U133A and U133B) for the MAS5.0 data. It will merge the data into one sample during the conversion.
Version 0.96.24.8: (11-20-2002) The ConditionChooserPlugin is now working (alpha) and is included in the distribution. Additional changes were made to MAExplorer to support it.
Version 0.96.24.7: (11-18-2002) Fixed Scrollbar initialization problem for the non-linear scrollers (p-Values, CV value, etc.)
Version 0.96.24.6: (11-15-2002) Fixed Q&A error in the command "Resize MAExplorer memory limits for the next time it is run" is in the (Edit | Preferences) menu. Added or debugged methods to MJAproperty and extended MJAcondition MJA API.
Version 0.96.24.5: (11-07-2002) Add command to resize the memory limits of MAExplorer. The command "Resize MAExplorer memory limits for the next time it is run" is in the (Edit | Preferences) menu. After the command is run, you must exit and restart MAExplorer for the new memory limits to take affect. It changes the memory limits in the MAExplorer.lax startup file.
Cvt2Mae Version 0.72.4 (11-07-2002) Fixed bugs in "Define Gipo Fields" where it would be be available under certain conditions. Also fixed another bug introduced with the addition of the MAS5.0 data.
Cvt2Mae Version 0.72.3 (11-05-2002) Increase buffer sizes to fix problem for very large input files with large gene descriptions.
Version 0.96.24.4: (11-03-2002) Fixed bug in non-linear sliders in State Scrollers. This had affected the values for the p-value and CV value. Extended functionality of popup State Scrollers sliders window. You can now toggle between all sliders, even those not active, and only those that are active.
Cvt2Mae Version 0.72.2 (11-02-2002) Fixed bugs in Affymetrix MAS5.0 where the "Define Quant Fields" were not being mapped automatically and separate files were not converting correctly.
Version 0.96.24.2: (10-24-2002) Added (File | Update Plugins) operation. It will prompt you on whether you want to update each default plugin one by one.
Cvt2Mae Version 0.71.2 (10-23-2002) Moved the name of the available Cvt2Mae.jar version number to the popup dialog query when doing the "Update Cvt2Mae" operation.
Version 0.96.24: (10-22-2002) Extended the number of grid groups from 52 [A-Z,a-z] to 152 [A-Z,a-z,1-100]. Moved the name of the available MAExplorer.jar version number to the popup dialog query when doing a (File | Update MAExplorer) operation.
Version 0.96.23: (10-21-2002) Extended the MJAgene.java API class so MJAPlugins can set gene annotations and properties from the plugin using external data.
Version 0.96.22: (10-18-2002) Extended the (File | Update MAExplorer) command so that it reads the version number of the MAExplorer.jar file on the maexplorer.sourceforge.net server and displays it prior to requesting the user to finish requesting the update. This allows users to see if they want to do the update.
Cvt2Mae Version 0.71.1 (10-16-2002) Added a "Update Cvt2Mae" button. This will (1) backup the current Cvt2Mae.jar file as Cvt2Mae.jar.bkup; (2) copy the latest Cvt2Mae.jar file from the maexplorer.sourceforge.net Web site and replace your Cvt2Mae.jar file in your installation directory. Then when you restart MAExplorer, it will use the new version of the program. The much more time consuming alternative is to do an entire download and reinstallation from the Web site.
Version 0.96.21: (10-15-2002) fixed comments for (File | Update MAExplorer) to give the actual server it will use. Fixed default PseudoArray Image to use when have single Cy3/Cy5 sample to use (Red-Yellow-Green) display. Cvt2Mae Version 0.70.7 (10-15-2002) has a major re-indentation of the Java source code to make it easier to read using the convention describe in the previous revision.
Version 0.96.20: (10-14-2002) We added a "Define GEO Platform ID" command for arrays that were submitted to NCBI's GEO (Gene Expression Omnibus) for use with future MAEPlugins. You can now use the new "Update MAExplorer" command in the File menu. This will (1) backup the current MAExplorer.jar file as MAExplorer.jar.bkup; (2) copy the latest MAExplorer.jar file from the maexplorer.sourceforge.net Web site and replace your MAExplorer.jar file in your installation directory. Then when you restart MAExplorer, it will use the new version of the program. The much more time consuming alternative is to do an entire download and reinstallation from the Web site. This version also has a major re-indentation of the Java source code to make it easier to read. It uses the automatic java indentation engine in Fote 4.0 (2 spaces/tab, convert tabs/space, space before '{', no space before '(').
Cvt2Mae Version 0.70.6 (10-11-2002) Fixed bug in Configuration file generator.
Version 0.96.18: (10-09-2002) Changed popup HP chooser initial window sizing so it works more consistently across platforms.
Version 0.96.17: (10-04-2002) Fixed bug with DetValue slider (the test was reversed). Also increased the dynamic range and precision of value indicated. The default is to leave the Detection Value filter off. Changed the default PseudoArray Image if there is one Cy3/Cy5 sample from the intensity display to the sum of cy5 (red) and Cy3(green) channels.
Cvt2Mae Version 0.70.5 (10-03-2002) Fixed bug in Affy MAS4 converter when selected "Generate genomic IDs from Descriptiopn". Also fixed bug in Quant Field assignments so it now shows the "DetValue" field when it was selected by the DetValue checkbox in the Genomic Identifiers Wizard.
Version 0.96.16: (9-30-2002) Fixed bug with positive data filter whereby it defaulted to being on. This was changed so that you need to explicitly enable it in the Filter menu.
Cvt2Mae Version 0.70.4 (09-27-2002) Added GEO Platform ID support.
Cvt2Mae Version 0.70.3 (09-23-2002) fixing the ArrayLayout Affy MAS5 tmp file converter. It now appears to generate the temp file correctly and read it correctly. Need to verify the code generators for the GIPO.txt file. There was a problem with embedded double quotes and the MAS5 ALO was not correct. Also had to add the additional fields to the FieldMap when the tmp file is extended.
Version 0.96.15: (9-19-2002) Added a new "Filter by Spot Detection Value" data filter. This can be used with the new Affymetrix MAS5.0 "Detection p-value" mapped through the "DetValue" or "CorrCoef" field in the .quant file. The next version of Cvt2Mae after 0.70.2 will output the "DetValue" field.
Cvt2Mae Version 0.70.2: (09-18-2002) Added automatic delete of old default Affymetrix*.alo files when Cvt2Mae starts up. This was required since we changed the names to reflect the MAS-4.0 and MAS-5.0 versions of the analysis software. Without this, you would have multiple names for the same files in the Array Layout chip list.
Cvt2Mae Version 0.70.1: (09-17-2002) Fixed bugs introduced in 0.70. Added remap code to better handle MAS5.0 data.
Cvt2Mae Version 0.70: (09-15-2002) Added Affymetrix MAS5 array layout so it will map (Signal, Detection, Detection p-value) to (RawIntensity, QualCheck, CorrCoef) Quant data fields. Fixed bug in "SwissProtID" data parser.
Version 0.96.14: (9-14-2002) Fixed incorrect base URL in "Help" pull-down menu. It had pointed to the old MAExplorer Web site not the the new http://maexplorer.sourceforge.net/MAExplorer/. The same documents were always visible from the Web site, but this makes it more convenient.
Cvt2Mae Version 0.68: (08-30-2002) Fixed bugs in Edit Layout where it was not always saving the changes you make to the state. Pressing Cancel in the Edit Layout restores the initial state before starting the edit. Pressing Back saves the state of the current panel you are working - previously only Next or Finish did that.
Version 0.96.12: Fixed bug introduced in version 0.96.11 such that it would pop up the dialog query when you did a "Open Disk DB" command.
Version 0.96.11: Extended MJAeval methods so can more easily invoke a new .mae startup file via a client-server MAEPlugin as well as the invokeCommand method. Modified internal methods and structures to support this.
Cvt2Mae Version 0.67: (08-15-2002) Fixed bug where the generated pseudoarray image was overiding the user specified (grid,row,column) geometry.
Version 0.96.10: Fixed bug in pseudoarray image whereby the current gene icon (yellow circle) sometimes was not reset properly for a database with X,Y coordinate data if the current gene was selected and you switched the current sample.
Version 0.96.08: Fixed bug in pseudoarray image whereby the current gene icon (yellow circle) sometimes was not reset properly if you toggled the mouseover checkbox, selected a different sample using the sample list in the pseudoarray image, or scrolled the pseudoarray.
Version 0.96.07: Fixed bug in font size updates for the pseudoarray image and scatter plot. Added methods to MJAproperty to get font size and font familiy.
Version 0.96.06: Modified data filter property bits for Gene, MJAgene, and Filter to make them more consistent when writing MAEPlugins.
Version 0.96.05: Fixed bug in data filter that caused problems with FilterPlugin's.
Version 0.96.04: Fixed bug when run database with no startup database, it does not refresh spot lists in the PseudoArray image.
Version 0.96.02: Fixed bug when run database with no startup database and no default MGAP demo database. It now lets you search the disk to find a .mae startup file instead of aborting with a Dryrot error. Fixed bug with chooser where it sometimes fails to let you access the last element of a list. The NCI/LECB site and the SourceForge site now both have the same full installers with JDKs (except for AIX and HPUX) and with the MGAP database.
A Cvt2Mae Version 0.66: bug has been fixed that makes it easier to automatically find the first row of spot data when scanning the users data input data file. Previously, the user might have to manually enter that starting data arow number in the Edit Layout wizard.
Version 0.96.01: Initial release on . Note: The NCI/LECB site will have the same installers., but with JVMs if you want to download a version with the JVM for your computer. The SourceForce does not have the JVMs because of space limitations.
Version 0.95.20: Inserted Open Source License into all code.
Version 0.95.19: Changed default for (File | Save file DB) and (File | SaveAs file DB) so that it saves all samples in the new .mae startup file - not just the samples in HP-X 'set', HP-Y 'set or in HP-E 'list'. Made the three status lines in the main window non-editable.
Version 0.95.18: Maintenance release. The Open Java API has been changed in the mjaGeneList, mjaGene, mjaEval classes.
Version 0.95.17: Maintenance release. The Open Java API has been updated and now includes working updateCurGene(), updateFilter(), updateSlider(), updateLabel(), and close() methods as well as new methods in the MJAgeneList API class. The stable release is now the version with the MaeJavaAPI active. The previous stable release 0.95.04 did not have the API.
Version 0.95.16: Maintenance release.
Version 0.95.15: Maintenance release to fixed FilterPlugins so the FilterTestPlugin example is working. Fixed bug recently introduced that prevented selecting spot in pseudoarray image.
Version 0.95.14: Fixed bug recently introduced that prevented menu commands from working correctly.
Version 0.95.12: Maintenance release. Changes to help support MAEPlugins and additional functions in the Open Java API. Fixed Quant input data parser bug so it now handles strictly lower-case letters for (Grid,Row,Column) data.
Version 0.95.11: Maintenance release. Changes to help support MAEPlugins and additional functions in the Open Java API.
Version 0.95.10: Maintenance release changes to help support MAEPlugins and additional functions in the Open Java API. Menu Plugin command is enabled to load MAEPlugins built using the Open Java API (under construction).
Version 0.95.08: Maintenance release to help support MAEPlugins and additional functions in the Open Java API. Menu Plugin command is enabled to load MAEPlugins built using the Open Java API (under construction). Added Plugins/ folder to distribution that is installed where you install MAExplorer. It contains several alpha-level JAR file plugins that work with the (Plugins | Load Plugin) command. We will be releasing the source code soon as the Open Java API alpha release in put on the MAEPlugins Web site.
Version 0.95.05: Maintenance release. Changes to help support MAEPlugins and additional functions in the Open Java API. Menu Plugin command is enabled to load MAEPlugins built using the Open Java API (under construction). Added (Plugins | Test Plugin Code) to invoke code for a plugin a debugging context (maintenance).
Version 0.95.04: Same as Version 0.95.03 optimized. It was compiled with the optimizing Java compile without debugging symbol tables. All Plugin support codes was removed. This results in a MAExplorer.jar file of 449Kb vs 599Kb for. Since the MGAP Web site Applet version can not use Plugins, this version is optimized for Applets and is to preferred over the Beta 0.95.03 version for now.
Version 0.95.03: Maintenance release. Changes to help support MAEPlugins. Menu Plugin command is enabled, but will only load MAEPlugins built using the Open Java API (under construction).
Version 0.95.01: Increased the number of spots/array that may be used from 16K to unlimited. Maintenance release. Changes to help support MAEPlugins.
Version 0.94.15: Fixed bug where occasionally, it would not load additional samples from the (Samples | Set Samples from Lists | ...) commands.
Version 0.94.14: Maintenance release. Changes to help support MAEPlugins. This release fixes a menu-related bug that occured if you used (File |Open File DB) to switch to a different database or to start the initial database rather than starting directly from the .mae startup file. The problem was that some of the sub menus generated might not correspond to the type of database. For example, if the previous database was an intensity database with duplicates F1 and F2, switching to a Cy3/Cy5 database might have some of the menus still appear as (F1/F2).
Version 0.94.12: Maintenance release. Changed placement of magenta circle marker so it is more visible in ClusterGram when selecting genes in the dendrogram/ClusterGram for the EGL by clicking on a gene with the Control key pressed.
Version 0.94.11: Fixed fatal error introduced ni 0.94.10 that occurs if you start the database with no data. Version 0.94.10 did work if you started it with a particular .mae startup file.
Version 0.94.10: Maintenance release. The "Filter by positive Quant data" toggle checkbox in the (Analysis | Filter menu) is enabled for all databases - not just those requesting it. If the database has 2 channels (F1, F2) or (Cy3,Cy5) each channel is checked. If the background correction is enabled, the background corrected values are tested to see if any of them are negative. Changed the labels in the scatter plot so that instead of displaying the current gene values as intensX= and intensY= or intens'X= and intens'Y= , it now displays it as X= and Y= or X'= and Y'=. The ' indicates that background correction is active. A new (Analysis | Plot | Show Microarray | "Scale pseudoarray image by 1/100 to zoom low-range values) command has been added to rescale intensity and (Cy3+Cy5) and (HP-X + HY-Y) (Red-Yellow-Green) plots to so low values are easier to visualize.
Version 0.94.09: Maintenance and Reference Manual update. Added copy of "Show 'Edited Gene List'" to Edit EGL submenu so easier to find.
Version 0.94.08: Changed button layouts on popup plots so it is easier to resize them to remove the right part of the plot if you want to conserve screen space.
Version 0.94.07: Fixed bug recently introduced in the histogram plots which prevent them from working. Fixed another histogram plot bug where the frequency count for "><" thresholding was reported incorrectly.
Version 0.94.06: Added the saving of the current values of all of the State Threshold scrollers when the (Edit menu | Preferences | Adjust all Filter threshold scrollers) in the message logging area when the State Thresholds popup window is closed. The Cvt2Mae (Version 0.60) has been extended to now handle Scanalyze data files as well as supporing a separate GIPO input data file.
Version 0.94.05: Added logging of MAExplorer messages to buttons in popup plots and reports. Fixed bug where old fixed gene sets for empty wells were not always restored correctly fro the previous state.
Version 0.94.04: Added logging of MAExplorer messages and command history in popup windows in the View Menu as "Show log messages" that occur during a session and "Show log of command history" respectively. The windows may be saved in log files. Added additional error detection of bad (field,grid,row,column) data when reading the GIPO and Quant files.
Version 0.94.03: Maintenance release for improving MAEPlugin support.
Version 0.94.02: Minor bug fixes related to the renaming of HybProbe to Samples menus. Also, extensive update of reference manual in both text and figures to showing many of the renamed menus so it is synchronized with the program.
Version 0.94.01: Major version release.
Renamed all previous references in the program to "hybridization probe" or "hybridization sample probe" to the new term "hybridized sample" for clarity. Changed many "HybProbe Menu" to "Samples Menu" and also many menu selections as well as plot and report labels to reflect this change. We are in the process of updating the manual computer screen figures and PDF slide presentations so that "hybridization sample probe" is shown as "hybridized sample". Also fixed other minor problems including fixing the inverted color scale for the "Pseudocolor Red(Cy5)-Yellow-Green(Cy3) Cy5+Cy3 ratio or Zdiff" command.
Version 0.93.03: Minor reorganization of (Plots | Clusters) submenus. This is the last release using the "HybProbe" menu.
Version 0.93.02: Beta-test of JDK-1.3 MAExplorer.jar file and new InstallAnywhere 4.5 installer. This adds JDK-1.3 installers for MacOS-X, IBM AIX, HP-UX, Linux. However, MacOS 8.1-9.x use the MRJ-2.2.5 JDK1.1.8 library. It also fixes a problem recently found running MAExplorer on some Windows-NT systems.
Version 0.93.01: Major version release.
Moved "Cluster Plots" submenu of the "Plots" submenu up one level in the "Analysis" menu.
Version 0.92.24: Maintenance and added more Plugins support. Top level Plugins menu appears, but is disabled in production version.
Version 0.92.23: Maintenance and changed names of some commands and some messages. Major edit of Reference Manual including expanded table of contents.
Version 0.92.22: Last Stable Release.
Major version release. Optimized colors in grayscale display for "Pseudocolor (HP-X,HP-Y) 'sets' p-value". Fixed error and optimized t-test computation.
Version 0.92.21: Changed grayscale display for "Pseudocolor (HP-X,HP-Y) 'sets' p-value" to display it as a color spectrum. Changed data displayed so p-Value is in the front of the list when you click on a spot etc. Added tests to disallow this display unless the data supports it.
Version 0.92.20: Beta testing new pseudoarray image display "Pseudocolor (HP-X,HP-Y) 'sets' p-value" that displays a gray value proportional to the p-Value in a t-Test of the HP-X 'set' vs HP-Y 'set'.
Version 0.92.18: Improved EP plot labels so it no longer prints the "MID:" prefix. Improved spot features list so it no longer prints the "plate[null,null,null]" if the plate coordinates are not present in the GIPO file.
Version 0.92.17: Fixed a bug which incorrectly computed the max and minimum ratio Cy3/Cy5 ratio values if the data allows negative intensity on these channels after background subtraction. This is required to support the GenePix array data format converter in the new version of Cvt2Mae (11-24-2001).
Version 0.92.15: A new (Edit | Preferences) command Adjust all Filter threshold scrollers - popup the state scroller window with all of the thresholds. This is useful when you want to adjust thresholds before you enable data Filtering or clustering. A bug was fixed where the state of the previous clustering method was not always cleared if you aborted clustering by clicking on the delete window button (eg. in Windows or the Mac). Click on a row with the Control (Shift) key pressed in the ClusterGram for hierarchical clustering will add(remove) that gene to(from) the Edited Gene List. If the (View | Show 'Edited Gene List') is enabled, then it will draw a magenta '*' before the gene name to indicate that you have selected it. This lets you select a particular subset of the genes from the hierarchical cluster. The Cvt2Mae data converter now has an alpha-release to let you convert non-standard data using the <User-defined> data option.
Version 0.92.14: The name of sample names and sample file names IDs has been made more flexible. If the "Database_File" is longer than 32 characters, there may be problems reading that file with MacOS-8/9. Therefore, you can use the "DatabaseFileID" to specify the "Database_File" (in which case they would be the same). Then, the labels used for the samples are the "Sample_ID" fields. This is upwards compatible with the previous method which used the "Database_File" for both the file name and the label name. The Reports of Highest (Lowest) Cy3/Cy5 data for a single sample were not easily accessible and this has been fixed. Alternate names for automatic detection of ESTs, ESTs similar to named genes were expanded and also includes the "EmptyWell" gene set (i.e. spots with no genes) (see Automatic Gene Class naming based on Gene Name in Appendix C Table C.4.1). A clustering option was added, Use median instead of mean for K-means clustering, of mean when computing K-means clustering (Bickel, 2001)).
Version 0.92.13: Maintenance release. Changed per-sample Good Spot filter algorithm and the CV filter algorithm. Added options to filter by either "HP-X 'set'" or "HP-Y 'set'". Algorithm now uses filters "HP-X or HP-Y" and "HP-X or HP-Y 'sets'" rather than the previous "HP-X and HP-Y" and "HP-X and HP-Y 'sets'". Adding some of the missing state that was not being saved during a "SaveAs DB" operation when creating a checking .mae startup file.
Version 0.92.12: Maintenance release for Plugins.
Version 0.92.11: Maintainence release. Increased width of scrollable sample names selection windows so it is easier to see the details on long sample names.
Version 0.92.10: Maintenance release. Due to a problem that some users are experiencing with the Java Installer, we are reverting to the previous version 4.01 (that does not support Mac-x). We will resolve these problems as soon as possible. Also fixed a problem with the Pseudocolor Red(Cy5)-Yellow-Green(Cy3) Cy3/Cy5 ratio or Zdiff which is now resolved.
Version 0.92.09: Maintenance release. Distribution of Java application with InstallAnywhere 4.5 (previous was version 4.0.1). This now supports MacOS-X, other Unix systems and may fix some other installation problems.
Version 0.92.08: Fixed bug in Edit use (Cy5/Cy3) else (Cy3/Cy5) for each HP command in HybProbe menu that changes were not saved in the state. Fixed bug introduced in HP Cy3 vs Cy5 intensity scatter plot.
Version 0.92.07: Added display of Cy3 and Cy5 channel intensity when click on gene in Pseudocolor Red-Yellow-Green Cy3/Cy5 ratio or Zdiff mode. Also added additional support for plugin installation from Configuration DB and .mae startup files.
Version 0.92.06: The Pseudocolor Red-Yellow-Green Cy3/Cy5 ratio or Zdiff - display the Cy3 and Cy5 microarrays as a pseudocolor image as the sum of Cy3 (Red) and Cy5 (Green).
Version 0.92.04: Internal changes. Also fixed bug in reading Affymetrix data converted with Cvt2Mae in the case where there is no genomic identifier and the "Location" is used as the genomic identifier.
Version 0.91.03: Made configuration database "swapRowsColumns" default to FALSE. This should probably never need to be true except for the initial MGAP database. If this flag was not set to false in previous configuration DB files, it would swap rows and columns in the pseudoarray image display.
Version 0.91.02: maintenance revision.
Version 0.91.01: Major version release.
This corrects a few minor bugs including crashing when starting up an empty database (that bug was introduced sometime in the last month). It is the first release with some reorganized code.
Version 0.90.08: Fixed bug in "Filter by 'Good Spot data'" where the initial "Check spots for Good Spot mode" was not properly initialized.
Version 0.90.07: Additional fixes in QualCheck mapping now handles the three types: Alphabetic codes, MAExplorer integer property codes, continuous floating point monotonic quality value. If the latter is used, then a "Spot Quality threshold" slider will popup when it is invoked. The MAExplorer Plugins Web page is also available at thei Web site and will track progress with the development of the MAExplorer Plugins Open Java API for investigators adding their own analysis methods.
Version 0.90.06: Fixed bugs in Genomic database popups. It was ignoring the request to popup a web page for particular genomic IDs.
Version 0.90.05: Added QualCheck mappings of Affymetrix "Abs Call" of "P" (or "G" or "T") to Good Spot, "A" to Bad Spot, and "M" (or "B" or "F") to Marginal Spot. This allows the "Filter by 'Good Spot data'" to handle this type of data.
Version 0.90.04: Added experimental GenomicMenu/URL configuation options for future use.
Version 0.90.03: Added QualCheck data filter for "Filter by 'Good Spot data'". This will be active if the QualCheck data is available in the .quant files.
Version 0.90.02: Fix bug in some of the State scroller controls when adjusting a scroller latches into a fixed state that can only be changed by restarting MAExplorer. Added LocusLink popup Web pages from LocusID (if it exists) or LocusLink from GenBank identifiers.
Version 0.90.01: Major version release.
(very Beta) Changing convention so use "MasterID" as the master gene index. This makes it more flexible than when used the CloneID as the master gene index. Added LocusLink.
Version 0.89.41: Added new scatter plots for comparing Cy3/Cy5 ratio data to compare either Cy3 or Cy5 of HP-X against Cy3 or Cy5 for HP-Y. Added additional change limit constraints "Compare channels meeting range" to "Filter by spot intensity [SI1:SI2] sliders". This allows partial filtering by spot intensity.
Version 0.89.40: Some of the State Scrollers were too sensitive at low values. Therefore, we set them to respond non-linearly with a more precise vernier at the low end.
Version 0.89.39: Fixed bug t-Test if using multiple samples with arrays with 1 Field.
Version 0.89.38: Fixed bug in Filter that allows the user to use either "positive only" or "positive or negative" intensity data (used with Affymetrix data).
Version 0.89.37: Increased the dynamic range of the scrollers for p-value, cluster distance, [Z1:Z2], |Diff XY|. Fixed labels in the Cy3 vs Cy5 plot so they are updated when the current sample changes.
Version 0.89.36: Fixed error in "Inside Range" for "Filter by Ratio ..." and "Filter by Cy3/Cy5 Ratio ...". Fixed HP-X,Y,E labels in the popup HybProbe menu "Choose HP-X,Y,E ..." command. Also added a new button "<< that removes all entries from the Selected list to the Remainder list. Changed the way the Cy3 vs Cy5 (for ratio data) or F1 vs F2 (if you are using intensity data where all spots are replicated) scatter plots work - the HP-X vs HP-Y scatter plots are not changed. The data Filter still works for all of the plots. Changed the name of the "NPN clustering" method in the menus and reports to "K-means clustering" since that is essentially what it is.
Version 0.89.35: Improved HP sample ID reporting in various lists, lists, etc. Added HybProbe menu command "Edit use (Cy5/Cy3) else (Cy3/Cy5) for each HP" for use with ratio data. This selectively swaps (Cy3,Cy5) data entries so may use (carefully!) dye-swap data for replicates. Added UP/DOWN buttons in the HP chooser to make it easier to adjust the order of the HP-E list.
Version 0.89.34: Changed the pseudoarray image generation paradigm so that it uses a fixed size spot and spacing and makes the pseudoarray image size dependent on the number of grids, rows, columns and fields. This results in a more consistent interface.
Version 0.89.33: Added "Filter by Cy3/Cy5 HP-X ratio or Zdiff sliders" to the Filter menu. This is useful for filtering data from a single sample.
Version 0.89.31: Added Rename command for Gene Sets and Condition lists. Added "SaveAs GeneSets" to K-means clustering. This saves all of the clusters as named Gene sets ("Cluster #1", "Cluster #2", etc.);
Version 0.89.30: Fixed problem with popup Web browser for Macintoshes.
Version 0.89.29: Optimized sorting on startup so it starts much faster when working with large arrays.
Version 0.89.28: Gene set and Condition set operations now let you select the sets by a pull-down choice menu as well as by typing in names of sets. Additional error checking added for input data files.
Version 0.89.26: Enhanced configuration file parser and sample name menu default; better error checking on input files to help catch some errors in manually edited user data files.
Version 0.89.25: Fixed configuration parser errors when reading non-standard data.
Version 0.89.24a: Fixed data for MAExplorer MGAP demo.
Version 0.89.24: Fixed bugs in popup browser to use GenBank ID (if it exists) with NCBI server, else it uses the Clone-ID (if it exists) with the nciarray cloneID-to-GenBank server.
Version 0.89.22: Fixed bugs in ClusterGram, saving current Gene Class.
Version 0.89.21: Fixed bugs in HP Chooser, Pseudocolor Red-Yellow-Green HP-XY plot menu, HP vs. HP correlation Report.
Version 0.89.20: Added correct scale for (Plot | Show Microarray | Pseudocolor Red-Yellow-Green HP-XY ratio or Zdiff).
Version 0.89.19: Added (Plot | Show Microarray | Pseudocolor Red-Yellow-Green HP-XY ratio or Zdiff) command to display the X and Y data as an additive sum of red (HP-X) and green (HP-Y) data.
Version 0.89.18: New version of download Java installer program that improves portability on different platforms (eg. MacOS, etc). Minor changes (spelling errors in parts of the program). Improved documentation.
Version 0.89.17: Added commands and functionality to a) find all copies of a named gene in the guesser using the SetE.G.L. button, b) added the "Replicate genes" GeneClass, c) added the "Filter by Genes with replicates" data Filter.
Version 0.89.16: Fixed several consistency checks when reading non-standard array data.
Version 0.89.15: Ignore enclosing space characters in SamplesDB, Configuration and .mae startup files.
Version 0.89.14: Fixed bug in Gene guesser when press the "Done" button. It sets the gene, but did not update the pseudoarray image. Disable genomic browser options in View menu if dbEST3'/5' or GenBankAcc3'/5' is not in the GIPO file database. Since GenBank and dbEST may be accessed via the mAdb Clone report or UniGene report, this should not be a problem. In the Reference Manual a) figures were updated for Genes instead of the older notation of Clone (Version 0.88.*); b) the Short Tutorial (Appendix A) was updated and clarified.
Version 0.89.12: Added "/Report" directory to hold SaveAs text (.txt) and plot window image (.gif) files. Improved fatal error (called DRYROT errors) reporting. Additional parts of the state saved.
Version 0.89.11: Added "Filter by positive quant. data" to filter out raw quantified data with negative values which may occur with some types of arrays. Also improved some of the popup window updates when the data Filter, normalization, EGL, or current clone changes.
Version 0.89.10: Fixed bug in correlation coefficient computation so it works correctly with all Gene Classes and data Filter.
Version 0.89.09: Fixed bug in reading configuration file that occurs if SubMenus are omitted. Fixed bug recently introduced when updating the finding clones similar to the current clone.
Version 0.89.08: Fixed bug in auto-update of List of Gene Sets when used with adding(removing) genes using the Control(Shift) clicking on a gene in the array image, scatter plot, etc.
Version 0.89.07: Fixed bugs in state saving.
Version 0.89.06: Save the full State when do a (File | SaveAs DB). The full state is restore when you startup the database you saved. Corrected bug in Gene Set Difference operator. Clarified some menu option names. Can now set # genes to report or Filter in a highest/lowest ratio genes in (Filter | Set max # genes in highest/lowest report). Added Report for (Report | Genes in 'Normalization Gene List').
Version 0.89.05: Added information fields in HP chooser.
Version 0.89.04: Corrected bug in Ratio Median correction option if using ratio data (i.e. Cy3/Cy5). Improved scatter plot labeling.
Version 0.89.03: Optimized the main screen area usage. Corrected data-dependent bug which sometimes occurs with the Use Ratio Median correction option if using ratio data (i.e. Cy3/Cy5).
Version 0.89.02: Set the Use Ratio Median correction option if using ratio data (i.e. Cy3/Cy5).
Version 0.89.01: Major version release.
Because MAExplorer can be used with both spotted clone arrays and oligo arrays,we renamed clones as genes (except where Clone ID is used) in both the MAExplorer program and in the Reference Manual.
Version 0.88.08: Enabled saving the name of the last project when you exit so it knows which file to use as a default when you do an "Open disk DB". Fixed the mnX/mnY data in XY-Statistics Report. Fixed title update in main window when open a new database. Also has fix for Linux Java installer (tested on Red Hat Linux version 6.0).
Version 0.88.07: Disabled the (File | Set Project) command as there is occasionally a problem with reading the maeProject.txt database file which causes it to hang. This should not be a problem for users with multiple databases as you still get the popup startup file browser when you invoke (File | Databases | Open file DB).
Version 0.88.06: Edit submenu "Sets of Conditions" HP lists is working and is saved/restore with the File menu "Save disk DB"/"Open disk DB".
Version 0.88.05: Added mouse-over to main window and moved gene locator button to left. Added "Use ratio median correction" option to Normalization menu. This option can be used for rescaling Cy3, Cy5 intensity data if the medians are unequal. Also, the manual has been updated and more discussion on data mining has been added.
Version 0.88.04: Edit submenu "Sets of HybridProbes" Condition lists are partially working (not working with File menu "Save disk DB"/"Open disk DB", set operations not enabled yet).
Version 0.88.03 Edit submenu "Sets of clones" and File menu "Save disk DB"/"Open disk DB" Save/Restore clone sets as .cbs clone bit set files in stand-alone.
Version 0.88.02: cleaned up SamplesDB.txt and MaExplorerConfig.txt specifications and sample files in Appendix C.
Version 0.87.08: Fixed some bugs in HP-X,-Y,-E chooser. Added additional checking for missing field names in data files. If a field is incorrect, MAExplorer can't continue. It now gives a popup "Dryrot" error message to give us information about which fields are incorrect.
Version 0.87.06: May now use combined chooser for selecting the active HP-X, HP-Y and HP-E probes.
Version 0.87.05: May now save all popup text windows as .txt files in stand-alone mode.
Version 0.87.01: May now save all plot windows as GIF images as .gif files in stand-alone mode.
Version 0.86.36: Fixed bug in "Filter by spot intensity [SI1:SI2] sliders". Allow simultaneous viewing of HP-X vs HP-Y and Cy3 vs Cy5 (or F1 vs F2) scatter plots. You may now also simultaneously view and HP-X/HP-Y and Cy3/CY5 ratio histograms.
Version 0.86.35: A new "Filter by spot intensity [SI1:SI2] sliders" mode has been added to the Filter menu. It is useful for filtering individual changes when analyzing Cy3/Cy5 data.
Version 0.86.34: The new stand-alone distribution is now generated with InstallAnywhere 3.5 instead of 3.5 beta. This corrects some of the problems we had seen with very large core images.
Version 0.86.34: The handling of "Out of memory errors" seen when clustering large numbers of clones on a small computer has been changed. Previously, it shut off the cache and continued the computation - although VERY slowly. Now, it prints out the following message:
```
 There is not enough memory to cluster current filtered clones. Options:
    1. reduce the number of filtered clones and try again, or,
    2. disable cluster-cache (Clustering menu) - will be VERY slow.
```
Version 0.86.33: A new "Set project" command has been added to the File menu. It selects the current project, if multiple projects have been set up (using the future "New project" command).
Version 0.86.29: A new "Show mouse-overinfo" mode has been added to the View menu (default is on). It reports HP probe and spot/clone details in the array image, scatter plot, expression profile overlay plot, etc.
Version 0.86.27: In stand-alone mode, the "Open disk DB" now lets the user open a .mae startup file. The user browses the local file system to select the startup file to use.
Version 0.86.25: When using ratio (i.e. Cy3/Cy5) data, the menu entries, plot and report legends change the names from (F1,F2) to (Cy3,Cy5) where appropriate.
Version 0.86.24: Corrected bug in using the ratio and intensity thresholding of mean HP data was previously using the single probe data.

4.3 Web Browser problems when running MAExplorer as an applet

Because MAExplorer is a large system, and there may be occasional problems running it in some Web browsers on some operating systems. We recommend you run MAExplorer as a stand-alone application as it is more robust.

Normally, MAExplorer works well as an applet with Netscape 4.7 or Windows Internet Explorer 5.0 on Windows PCs and on SUN Unix. It does not seem to work well as an applet on Macintoshs and problems have been reported on SGI systems.

One solution is install Sun's HotJava browser. The HotJava browser is available from Sun Microsystems . You can download HotJava for the Windows-95/-98/-NT/-2000/-XP and for Solaris (Unix).
Reguardless of which browser is used, because it is is doing a lot of computation, MAExplorer runs best on a fast machine with lots of memory. This is especially true when running a browser because of the additional browser overhead.

4.4 Handling fatal error reporting (i.e. DRYROT errors)

If you encounter a fatal error that is detected by MAExplorer, it will popup an error reporting window. We call this a "DRYROT" error (thanks to "S.A.I.L." - Stanford AI Lab) because something is wrong in the program or in the user's data files and from which it can not recover. This type of error should not have happened. Please save and e-mail the report to us so we can try to fix the bug or diagnose the problem. The following figure shows an example of part of a DRYROT error report.

Figure 4.4 Example of a fatal Dryrot Error window. This may occur for a variety of reasons. This window lists the main reason and also lists some of the MAExplorer state information. If you wish, you may save this window (press the "SaveAs" button) and mail it to us. We may try to correct the problem in the next release if it is a problem with MAExplorer. Alternatively, it could be a user data error.

Example of a fatal Dryrot Error after SaveAs

Figure 4.4.1 Example of a fatal Dryrot Error window after SaveAs. This tells you where the saved error message file was saved and the email address to send it to if you wish.