View and Download Affymetrix Microarray Data

File types available for downloads

We perform three independent experiments for each experimental condition and time point under study. For each sample, the files necessary to analyze the raw and processed data are combined in a *.zip file that is downloadable from this website. Zip files can be easily decompressed by a variety of software tools as Winzip or StuffIt Expander that are freely available through the web.

Each *.zip file contains three different data files for each genechip: *.dat, *.exp, and *.txt files. In addition, we provide QC.xls summary files that contain Affymetrix data for all arrays related to one experiment for data quality assessment.

*.dat - data file

This file type can only be used with Affymetrix MAS4.0 or GeneChip Software tools!

It contains the image of the scanned array, corresponding to the raw hybridization data. These data are not processed, and no scaling factors or normalization is embedded.

*.exp - experimental information file

This file type can only be used with Affymetrix MAS4.0 or GeneChip Software tools!

This file contains the experimental information for each array including the experiment name, sample, and the type of array being used. Affymetrix software uses the *.exp file together with the *.dat file to process the raw data in order to generate data analysis files.

*.txt file - analysis output file

This is an ASCII text file that can easily be imported into standard statistical and spread sheet analysis programs like Microsoft Excel for your own downstream data analysis!

This file is the output generated by the analysis of a *.dat image file using Affymetrix MAS4.0 software. It contains the absolute analysis, which determines whether a transcript is present (P) or absent (A) in a sample. It also provides the Average Difference (AvgDiff) value as a relative indicator of the level of expression of a transcript.

Data in this file have been subjected to Global Scaling in order to be able to compare data from multiple probe arrays. The output of any experiment was multiplied by a Scaling Factor to make its Average Intensity equal to an arbitrary Target Intensity, set by Affymetrix for each probe array type, e.g. the Target Intensity for the Mu11K arrays is to be 1500. Researchers who wish to compare data that have been scaled to match a different Target Intensity should re-process the *.dat files with the appropriate Target Intensity before making comparisons between expression profiles.

QC.xls - quality control file

This file contains a summary of the experimental information generated by Affymetrix software for each probe array. It contains information about Average Intensity, Scaling Factors, and Normalization Factors used for each probe array, which allow to assess the quality of the expression data.

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Page last modified: 07-Aug-2003