Biostatistics

File Descriptions
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This section gives descriptions of the Affymetrix® data files that are generated in the Microarray Core.  The file types described are as follows:


File Name
Extension
Data file .DAT
Cell file .CEL
Experiment file .EXP
Chip file .CHP
Expression analysis file .TXT
Report file .RPT
 

Data File (.DAT)

A .DAT file is the first file generated when a microarray is scanned.  It
is a table comprised of the fluorescence measurement and feature
identity for each pixel of a scan.  A microarray feature is an area on
the array occupied by a population of oligonucleotide probes with the same sequence.  A feature is comprised of many pixels.

Cell Intensity File (.CEL)

The data in a .DAT file is processed to generate the values found in the
.CEL file.   A .CEL file contains a single value for each feature.  Each
value in a .CEL file is a statistical "summary" of the fluorescence from
a single feature.  The majority of the microarray data analysis programs, including dChip, MAT and Bioconductor, use the summary probe level values found in CEL files as the basis of their analyses.  The .CEL file contains the information for viewing the images that result from scanning the hybridized arrays.

Chip File (.CHP)

The .CHP file contains numerical estimates of the signal intensities, as well as presence calls, for each transcript on the microarray.  The expression estimates are calculated using the Affymetrix® “Statistical Algorithm" for absolute analysis. Alternative methods for generating transcript level expression estimates can be found in many other microarray analysis programs.

Expression Analysis File (.TXT)

The .TXT file is a text version of the .CHP file containing all of the same information in a tab-delimited format.

Report File (.RPT)

The Report File for expression arrays summarizes background noise, housekeeping information, spike controls and other quality control parameters.

The Report File for the 10K, 100K and 500K arrays infers gender from the X chromosome calls, summarizes the AA, AB and BB calls along with the overall number of calls, and provides other quality control parameters.  

Experiment Information File (.EXP)

The Experiment Information File is a text file containing sample information, fluidics settings and scanner settings.