Affymetrix File Descriptions
Affymetrix's program GCOS creates several files for each step of the data generation process. You may obtain a copy of GCOS if you would like to reanalyze files. Contact Anne-Marie Girard for more information. Data Transfer Tool should be used when sharing GeneChip data between GCOS users. It can be used to extract many of these Affymetrix files from the DTT file. It is available when you register with Affymetrix's NetAffx web site. Affymetrix Data Analysis Fundamentals Guide describes experimental design, assessing data quality, some statistics and data interpretation, along with their annotataion mining tools.
| File Extension | Description |
| *.dat | Data File is created when probe array is scanned. Consists of pixel information, a grid laid down over data points |
| *.cel | Cell intensity file is created when software computes a single intensity for each cell from the Data File (*.dat). This file is often imported into other programs, such as GeneSpring, for preprocessing, normalization and analysis. |
| *.chp | Chip File generated by analyzing the Cell Intensity file (*.cel) with tme MAS 5.0 algorithm |
| *.rpt | Report File summarizes data quality information generated from the Chip File (*.chp) |
| *.txt, *.xls |
Exported Text files generated from the Chip file (*.chp) in either text format or Excel file.The file called PivotDataExperimentName contains the data generated with GCOS software (sometimes called MAS5.0 method) with a scale factor of 500. It can be imported into GeneSpring. The file called ReportExperimentName contains the expression reports for all files in the experiment. They should be checked for consistency and quality across all chips. See pages 36-40 of the Affymetrix Data Analysis Fundamentals Guide. |
| *.cab | Cab File is a compressed file that is a backup copy of a project which may include samples and/or experiment and a process or publish database. This file can be extracted using Affymetrix software Data Transfer Tool |
| *.dtt | DTT archive file is an archive file type which is much faster and requires less space than the Cab file |
| *.cif, *.cdf, *.psi | Probe information or library files contain information about the probe array design, characteristics, probe utilization and content, and scanning and analysis parameters. These files are unique for each probe array type. The #.cdf file is often needed to extract Cell Intensity data using other data extraction programs such as RMA or dChip |
| *.jpeg | Image File of the data file exported |
| *.xml | MAGE-ML compliant XML file with CGOS experiment and sample attributes and data process |