Data Analysis - Affymetrix Arrays Overview
At the core of Affymetrix data analysis is GeneChip® Command Console Software, or AGCC, formerly known as GCOS and MAS 5.0. This is the software that controls the entire GeneChip® system. The fluidics station and the scanner are both controlled with this software. Therefore, the program creates several files for each step of the Affymetrix process. Affymetrix' Human Whole Transcriptome Array 2.0 will require the Transcriptome Analysis Console (TAC) Software for analysis. Please visit the Affymetrix website for more information.
|Experiment Data File Name||File Extension||Description|
|Cab File||.cab||This file is a compressed GCOS file that contains the .dat, .cel, and .chp files. In many cases the user will receive the .cab file instead of the .dat file in their link from the MAID request.|
|Data File||.dat||The image of the scanned array.|
|Cell Intensity File||.cel||The software derives the .cel file from the .dat file and automatically creates it upon opening a .dat file. It contains a single intensity value for each probe cell delineated by the grid (calculated by the Cell Analysis algorithm).|
|Chip File||.chp||The output file generated from the analysis of a probe array.|
|Report File||.rpt||The report generated from the analysis output file (.chp).|
|Experiment Information File||.tif||A standard file format for graphic images. The Microarray Suite software exports graphic images in this file format.|
|A standard format for text files. The Microarray Suite software exports text in this file format. It also can export the standard format for Excel files.|
Users can also click on the link below to view Data Analysis Fundamentals, two PDF files explaining the basics of Affymetrix data.
Again, we encourage all Affymetrix users and all those interested to register with the Affymetrix web site. It is free and it allows access to protocols, technical notes, manuals, and many other useful resources.