Supported platforms

MS Windows with Java Runtime Environment 1.4.2_04 or higher
MS Internet Explorer 6 is recommended

Analysis steps

1) Original CEL files are needed to use the tools of this website. CEL files are the raw data files (with .CEL extension in the filename) containing the intensity and standard error of each individual probes, and probe position. CEL file is created when you apply grid information with scanned Affymetrix GeneChip with GCOS software.

(Note: There are two versions of CEL file; version 3 and 4. You need version 3 CEL file, which is ASCII format. If you have compiled CEL version 4 file, it can be converted to version 3 with CelFileConversion Tool, which is available at Affymetrix website.)

2) Generate mask file: select minimum length of overlap for probe and minimum number of "valid" probes per probe set. Mask file for "Chip A" will be generated by clicking "Generate Mask File" button. The mask file for Chip B can be produced by selecting previous Chip B type for Chip A and vice versa. List of probe sets also can be generated with the same criteria.

3) Download the standalone executable Put_mask.jar here.Use the downloaded .jar program to combine the generated custom mask file with your CEL files.

4) Use GCOS (or MAS 5.0) or any other algorithm (dChip and Bioconductor affy package) to calculate expression index with your new CEL files. Of newly calculated expression index, those probe sets generated in previous step are most comparable.