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White Paper Documentation for Software Developers


The following white papers were developed to assist software developers to write applications for the Affymetrix platform.

Automating a Typical Affymetrix Workflow

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.

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Structure of the Genotyping Probe Set

This document describes the structure of the probe set used 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.

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Structure of the Expression Probe Set

This document describes the structure of the probe set used 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.

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Obtaining the List of Probe Sets

This document describes where and how to obtain the list of probe sets for an expression and genotyping array.

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Masking Probes Whitepaper

If you plan on developing algorithms to analyze intensity data in CEL files, this document will describe how the masked probes and probes sets are stored by the Affymetrix software.

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Parsing Tiling BAR/CHP Files

This document describes with sample code how to parse and extract information from a tiling CHP file.

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Parsing Genotyping CHP Files

This document describes with sample code how to parse and extract information from a genotyping CHP file.

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Parsing 3' IVT Expression CHP Files

This document describes with sample code how to parse and extract information from a 3' IVT Expression CHP file.>

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Parsing Exon CHP Files

This document describes with sample code how to parse and extract information from an Exon CHP file.

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Linking Files Through GUIDs

Learn how to determine file relationships using the GUIDs embedded in the Affymetrix GeneChip Command Console format files.

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Details on PGF/CLF Library 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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