Cvt2Mae Home | Description | Download | FAQ | Appendix | Example | Revisions | MAExplorer home | Help Desk

Example of Using Cvt2Mae to convert Some Affymetrix data for MAExplorer

This detailed example shows how one might convert Affymetrix data for use with MAExplorer. The example is presented as a series of computer screen shots. Similar screen shots are available as
PDF documents for other types of chip array layouts. The example is divided into three parts: specifying the input data files, editing the array layout, and generating the output data files for use with MAExplorer.

1. Specifying the input data files

Figure 1. shows the Affymetrix tab-delimited data in Excel. Figure 2. Initial state of the Cvt2Mae Program. Figure 3. Selecting a Chipset Array Layout. Figure 4. Selecting one or more user input data files by pressing the "Browse input file name" button. Then select a user input data file using the file browser. Figure 5. Files selected by user and samples "discovered" in the data file.

2. Editing the array layout

Figure 6. Edit Layout Wizard for name of the Array Layout with A) original and B) the new layout name. Figure 7. Edit Layout Wizard for Grid Geometry. Figure 8. Edit Layout Wizard for Starting Data Rows. Figure 9. Edit Layout Wizard for Ratio or Intensity data. Figure 10. Edit Layout Wizard for optional (X,Y) spot coordinates available in the input data. Figure 11. Edit Layout Wizard for optional Genomic ID values available in the input data. Figure 12. Edit Layout Wizard for optional Gene Names available in the data. Figure 13. Edit Layout Wizard for optional calibration DNA available in the data and UniGene species prefix. Figure 14. Edit Layout Wizard for optional user names for Project, Database, Sub-database, etc. Figure 15. Edit Layout Wizard for optional HP-X and HP-Y 'set' experimental class (i.e. condition) names. Figure 16. Edit Layout Wizard for changing the default data filter threshold slider values.

2.1 Specifying the mapping between your data file fields and those required by MAExplorer

There are two special wizards for specifying the mapping array layout GIPO and Quant input data field names. These mappings allow the converter to take your data specified in some columns (i.e. Fields) of your data input file and use it to generate standard MAExplorer output files. Figure 17. shows the Edit Layout Wizard for "Assign GIPO fields" used to generate the MAExplorer GIPO data file. Figure 18. shows the Edit Layout Wizard for "Assign Quant fields" used to generate the MAExplorer Quant files (one for each hybridized sample). Figure 19. shows saving modified Array Layout if you have made changes.

3. Generating the output data files for use with MAExplorer

Finally, the array layout has been defined and we can run the converter. Figure 20. Selecting the output folder in which to save the converted files. Figure 21. Browse to select the output folder in which to save the converted files. Figure 22. shows the interface after selection of the output file folder using a file browser. Figure 23. shows the conversion being performed after the user pressed the RUN button. Figure 24. shows the conversion summary instructions after the conversion is finished. Figure 25. shows the files that are generated by Cvt2Mae for use by MAExplorer. Figure 26. Starting MAExplorer on the converted data by clicking on Start.mae file. Note that the location of the "MAExplorer startup file:" in Figure 8. Go to that file and click on it to start MAExplorer. Alternatively, start MAExplorer and do "File | Open Disk DB" and open that file to start it up.


Figure 1. shows the Affymetrix tab-delimited data in Excel. (after missing fields have been edited as described above).




Figure 2. Initial state of the Cvt2Mae Program. The user must select an array layout or define one in order to analyze the input data file or files.



Figure 3. Selecting a Chipset Array Layout. The built-in array layouts are shown for the Incyte and Affymetrix. User-defined layouts would be added by selecting the <User-defined> layout.



Figure 4. Select one or more user input data files by pressing the "Browse input file name" button and then pick a file. If the layout indicates that it may contain more than one hybridization, it will attempt to find the data. You can subsequently rename individual samples which may be necessary if you are reading several files with the same sub-sample names. After the file browser pops up, select a user input data file. If you are using a file that contains all of your samples, then you only need to specify one file. If you have several files, then repeat this step until you have added all of the files you want.



Figure 5. Files selected by user and samples "discovered" in the data file. Each input file is analyzed to determin if it has] multiple samples and if so they are added to the list of input files at below step 2.1 in the window. You may remove any samples which may be necessary for bad data. You may rename any sample which may be necessary if you have the same sample name occuring in several different data files (they are actually different samples).



A)

B) 


Figure 6. Edit Layout Wizard for name of the Array Layout. A) is the original array layout frome the database. B) Since we may want to edit it, we will rename the vendor and Array layout name. This will enable us to save the changed layout if we wish. You may not overide system defined layouts, but you may overide your own layouts or save a system layout under a new name (as is shown here).



Figure 7. Edit Layout Wizard for Grid Geometry.



Figure 8. Edit Layout Wizard for Starting Data Rows.



Figure 9. Edit Layout Wizard for Ratio or Intensity data.



Figure 10. Edit Layout Wizard for optional (X,Y) spot coordinates available in the input data.



Figure 11. Edit Layout Wizard for optional Genomic ID values available in the input data.



Figure 12. Edit Layout Wizard for optional Gene Names available in the data.



Figure 13. Edit Layout Wizard for optional calibration DNA available in the data and UniGene species prefix.



Figure 14. Edit Layout Wizard for optional user names for Project, Database, Subdatabase, etc.



Figure 15. Edit Layout Wizard for optional HP-X and HP-Y 'set' experimental class (i.e. condition) names.



Figure 16. Edit Layout Wizard for changing the default data filter threshold slider values.



Mapping Array Layout GIPO and Quant input data field names

In addition to the above global defintions, additonal Array Layout parameters need to be define. These are mapping of input file data field names for GIPO and Quant data to the names required by MAExplorer. There are two wizards for helping define these mappings. For the predefined Array Layouts these are already setup but may need to be defined or edited for user-defined data.

Figure 17. Edit Layout Wizard for Assign GIPO fields. These Gene-In-Plate-Order data field mappings should only be changed if required for additional data fields you may have added to your input file. All fields should be defined. (it is required for <User-defined> data). In general, it may be ok to have some non-critical genomic ID fields undefined.



Figure 18. Edit Layout Wizard for Assign Quant fields. These Quantification data field mappings should only be changed if required to define all fields (it is required for <User-defined> data).



Figure 19. Saving modified Array Layout if you have made changes. This is useful if you have changed the array layout with "Edit Layout", "Assign GIPO fields", or "Assign Quant fields" so that you can use it another time.



Figure 20. Selecting the output folder in which to save the converted files. The Magenta "Save Layout" button means that you may save the edited array layout if you wish. You now need to create an output folder to put the converted data. You may create a New Folder, use an Existing Folder or use the Same Folder that contained the input files. We selected the "New Folder" option.



Figure 21. Browse to select the output folder in which to save the converted files. You may create a new folder here. Select the "name" of the folder - don't go into the folder.



Figure 22. shows the interface after selection of the output file folder using a file browser. Notice that the current project directory is now displayed in the interface as well as the location of the MAExplorer Start.mae file that will be generated. The data will be created when the Run button is pressed.



Figure 23. shows the conversion being performed after the user pressed the RUN button. This process takes a minute or so depending on the speed of the computer and the complexity of the data.



Figure 24. shows the conversion summary instructions after the conversion is finished. At this point press the DONE button to exit the converter.



Figure 25. shows the files that are generated by Cvt2Mae for use by MAExplorer. The generated data consists of several directories that are described in the Reference Manual Appendix C.



Figure 26. Starting MAExplorer on the converted data by clicking on Start.mae file. Alternatively, Note that the location of the "MAExplorer startup file:" is specified. Go to that file and click on it to start MAExplorer. Alternatively, start MAExplorer and do "File | Open Disk DB" and open that file to start it.


MAExplorer [ MAExplorer home | Cvt2Mae home | Help desk | LECB/NCI/FCRDC ]