Data Analysis and Storage

The Affymetrix GeneChip® Operating Software (GCOS) controls the fluidics stations and the scanner. In addition, the GCOS acquires data, manages sample and experimental information, performs gene expression data analysis, and supports the GeneChip® DNA Analysis Software (GDAS) used for resequencing and mapping data analysis and report generation.

Each Affymetrix array consists of 3 files: *.EXP, *.DAT, *.CEL. Together, these contain the raw image data used for data analysis. The file in which the data is viewed is the *.CHP, which may be converted to a tab-delimited text file for easy uploading into data analysis programs such as Rosetta Resolver or GeneSpring. It is extremely important that you keep and back-up your copies of the 3 original files (*.EXP, *.DAT, and *.CEL) for each GeneChip®. The *.CHP may change depending on your expression analysis settings, but the raw data always remain the same.

Please visit the FAS Center’s Computational Biology page for information on software analysis tools. For assistance with Affymetrix software (GCOS or Microarray Suite), please contact Jennifer Couget.