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The following white papers were developed to assist software developers to write applications for the Affymetrix platform.
Overview of Automating Affymetrix Informatics Workflows From registering samples from an external database to pulling NetAffx annotations, this whitepaper provides a high-level overview of how informatics workflows can be automated on the Affymetrix Platform.
This document describes the structure of the probe set use by the 10K, 100K, 500K and other genotyping probe arrays.
Sample code, using the File SDK, is provided to extract PM/MM intensities from a CEL file organized by the probe set structure defined in the CDF file.
This document describes the structure of the probe set use by expression probe arrays.
Sample code, using the File SDK, is provided to extract PM/MM intensities from a CEL file organized by the probe set structure defined in the CDF file.
This document describes where and how to obtain the list of probe sets for an expression and genotyping array.
If you plan on developing algorithms to analyze intensity data in CEL
files, this document will describe the how masked probes and probes sets
are stored by the Affymetrix software.
This document describes the steps required for creating a GCOS or Command
Console format CHP file.
This document describes with sample code how to parse and extract information
from a tiling CHP file.
This document describes with sample code how to parse and extract information
from a genotyping CHP file.
This document describes with sample code how to parse and extract information
from a 3'IVT Expression CHP file.
This document describes with sample code how to parse and extract information
from an Exon CHP file.
Learn how to determine file relationships using the GUIDs embedded in
the Affymetrix GeneChip Command Console format files.
Details on PGF/CLF files for exon analysis are outlined in this whitepaper.
The following documents are available which describe the PGF, CLF and
BGP file formats.
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