MAExplorer Newsletter #5, January 15, 2002
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This newsletter is issued periodically to announce major changes and
enhancements to the MicroArray Explorer (MAExplorer).
Since you have expressed an interest in MAExplorer in the past, you
were included in this newsletter mailing. If you don't wish to receive
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Old newsletters are available in the Web site archive, so if you are
interested in following developments in MAExplorer but don't want the
E-mail you could get the information there.
WEB SITE: http://www.lecb.ncifcrf.gov/MAExplorer
CONTACT: mae@ncifcrf.gov
PHONE: 301-846-5535 (Peter Lemkin)
301-846-5539 (Greg Thornwall)
FAX: 301-846-5598
NEWSLETTER
ARCHIVE: http://www.lecb.ncifcrf.gov/MAExplorer/Newsletters/
Enhancements in the current Version 0.94.04 since the last Newsletter
=====================================================================
At the time of the last October 17, 2001 newsletter #4, the version
was 0.92.09.
There were a number of improvements and new features added as well as
the Beta-release of a data format conversion tool (Cvt2Mae). Details
on these features are described in the Reference Manual.
1. Installing MAExplorer
We now use the ZeroG Corporation InstallAnywhere 4.5 program to
install MAExplorer. MAExplorer is now distributed with JDK 1.3 Java
Virtual Machine rather than the older JDK1.1.8 used by the previous
versions. InstallAnywhere 4.5 requires this to work across all
platforms including MacOS-X, IBM AIX, HP-UX, and some new Unix
systems. This fixes several problems that have occurred with Windows-NT
and may fix some other installation problems.
2. Menu reorganization, name changes and new commands
-----------------------------------------------------
2.1 We reorganized the Analysis menu to make the user interface more
consistent. We moved "Cluster Plots" submenu of the "Plots" submenu up
one level in the "Analysis" menu.
2.2 A number of new gene data filters have been added. The (Analysis
| Filter | Filter per-sample Good Spot data) and the (Analysis |
Filter by spot CV) filters have been extended. New options for these
commands now allow filtering either by 1) "HP-X 'sets'" or "HP-Y
'set'", 2) by "HP-X or HP-Y", and 3) BY "HP-X or HP-Y 'sets'". The
previous filter only allowed filtering by "HP-X and HP-Y" and "HP-X
and HP-Y 'sets'".
2.3 You may now pre-edit the scrollable thresholds prior to using them
in data filters and clustering. A new (Edit | Preferences | Adjust all
Filter threshold scrollers) popups the state scroller window with all
of the thresholds available to adjust. 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).
2.4 A new pseudoarray image display command (Analysis | Plots |
Pseudocolor (HP-X,HP-Y) 'sets' p-Value) has been added. It displays a
pseudo color value proportional to the p-Value for in a t-Test of the
HP-X 'set' vs HP-Y 'set'. This only is available if HP-X 'set' vs HP-Y
'set' data is available.
2.5 Two new optional popup logging windows were added that log query
messages and response and command history. The (View | Show log
messages) command logs messages that occur during a session. These
could be the query and response when interrogating the database for
particular genes. The (View | Show log of command history) command
shows the commands you have invoked during your data mining
session. The windows may be saved in log files or cut and pasted into
other programs.
3. Clustering changes
---------------------
3.1 When using K-means clustering, you may optionally use the median
instead of mean when computing the center of a cluster by using the
(Analysis | Cluster | Use median instead of mean for K-means
clustering).
3.2 After you have created a ClusterGram using hierarchical
clustering, you can select a subset of genes that appear significant
to you in the ClusterGram and save them in the Edited Gene List for
further analysis. They do not need be contiguous. 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.
4. Data Conversion issues
-------------------------
4.1 The Cvt2Mae "wizard" data format conversion tool has been enhanced
and made more flexible. The <User-defined> data option is now
available to convert non-standard data. A default array layout has
been added for GenePix data. Since each array is different, this can
serve as a basis to define an array layout for your data that was
quantified using GenePix. This tool lets the user convert their array
data to MAExplorer format so it may be used with MAExplorer and is
described in the Cvt2Mae home page
(http://www.lecb.ncifcrf.gov/Cvt2Mae). The Cvt2Mae Affymetrix array
layouts offer the option of using genomic identifiers in the
Description field.
4.2 Restrictions on the length of sample file names has been removed
for MacOS 8-9. This resolves a potential problem for MacOS8/9
users. 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.
4.3. A new Gene Class "Empty Wells" has been added and contain a list
of empty spots on the array (i.e. spots with no genes or the names
"Empty", "EmptyWell", or "Empty Well"). Also, Alternate names were
added for easier automatic detection of ESTs, ESTs similar to named
genes were added. These changes are documented in the Reference
Manual (see Automatic Gene Class naming based on Gene Name in Appendix
C Table C.4.1).
4.4 Additional input data error detection of bad (field, grid, row,
column) data was added to MAExplorer when reading the GIPO and Quant
input files. This can be useful in detecting corrupted input data.
5. Documentation
----------------
5.1 The Reference Manual and tutorials have been revised to reflect
the renaming of Hybridization Probes to Hybridized Samples. It has
also been clarified and revised and new material added.
5.2 The Web page devoted to MAExplorer PDF (Adobe Acrobat) documents
has been updated.
5.3 The Web page for MAExplorer plugins describes and documents
MAEPlugins. http://www.lecb.ncifcrf.gov/MAEPlugins). Some initial
MAEPlugins are undergoing alpha-testing and will be made available on
this Web site.
Future enhancements under development
=====================================
* Added functionality in the Cvt2Mae data format conversion tool for
"User-defined" data.
* User extensible analysis methods using Java Plugins by having users
write to a MAExplorer Java plugin API (Application Programming
Interface. Check for status on the web page
http://www.lecb.ncifcrf.gov/MAEPlugins for more information.
* New data filtering methods
* New normalization methods
* New clustering methods
* Improved graphics
* Improved documentation and training films
* Access additional genomic Web databases
* Generation of extracted image spot regions for specific genes
across a set of samples
* etc.
Please contact us with your comments, suggestions and problems
running MAExplorer at mae@ncifcrf.gov.