Affymetrix Support

Golden Helix SNP & Variation Suite is an Affymetrix GeneChip-compatible application with support for importing genotype and intensity data from Affymetrix GeneChip arrays and associated library and annotation (marker map) files for SNP and copy number analysis.

Below are tips and commonly accessed files that will help you get the most from your Affymetrix data.

Supported File Types

The following is not an exhaustive list and is subject to change. Please contact support for the most up-to-date information.

For SNP analysis, SVS supports the import of CHP files from the following arrays:

Genome-Wide Human SNP Array 6.0
Genome-Wide Human SNP Array 5.0
Human Mapping 500K Array
Human Mapping 100K Array
Human Mapping 10K Array
Axiom Array

For CNV analysis, SVS supports processing of CEL files from the following arrays to compute LogR values for copy number analysis:

Genome-Wide Human SNP Array 6.0
Genome-Wide Human SNP Array 5.0
Human Mapping 500K Array
Cytogenetics Whole-Genome 2.7M Array

For the above arrays, various Affymetrix tools can be used to process CEL files and compute LogR, B-Allele frequency, copy number state and other values. These can be imported through the support of CYCHP, CNT and CNCHP files.

Additionally, SVS has a custom import script for the Molecular Inversion Probe (MIP) array: MIP CN Transformation Script

Tutorials

Read the following tutorial for step-by-step workflows on how to perform SNP and copy number analysis using Affymetrix arrays:

Test Data

For your convenience we have created a number of 100k and 500k Affymetrix generated data files, which include a fabricated phenotype variable. After downloading, these files need to be unzipped. The can be imported into SVS using the Import >Golden Helix Legacy GHD option.

500kCaseControlResponse.ghd.zip (48 samples)
500kContinousResponse.ghd.zip (48 samples)
100kCaseControlResponse.ghd.zip (90 samples)
CaseControl2880Patients100k.ghd.zip (2880 samples)
100kContinousResponse.ghd.zip (90 samples)

If you are interested in importing raw Affymetrix .chp files using HelixTree, feel free to download the following files. After downloading, these files need to be unzipped. They can be imported into SVS using the Import >Affymetrix >CHP option.

50KhindCHPFiles.zip
50KxbaCHPFiles.zip
250KnspCHPFiles.zip
250KstyCHPFiles.zip

5.0 and 6.0 Marker Maps/Annotation Files

Affymetrix 5.0 and 6.0 annotation files come in two separate files, one containing SNP probes and the other copy number probes. In order to properly process and analyze 5.0 and 6.0 data for copy number analysis you need the set merged and imported into SVS.

If you are having trouble downloading the latest Affymetrix annotation files using the NetAffx service, you can download them here for the 5.0 and 6.0 arrays.

Note: These files may not always be up to date.

For Affy 5.0 click the following link: www.goldenhelix.com/download/bin/Affy_SNP5_MM.zip
For Affy 6.0 click the following link: www.goldenhelix.com/download/bin/Affy_SNP6_MM.zip

Library Files

If you are having trouble downloading the latest Affymetrix library files using the NetAffx service, you can download them here for the 5.0 and 6.0 arrays.