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" 'Where is the missing heritability?' is a question asked frequently in genetic research. The difficulty seems to come down to the common disease/common variant hypothesis not holding up." » Read more
Affymetrix Support
Golden Helix SNP & Variation Suite is an Affymetrix GeneChip-compatible™ application with support for directly importing Affymetrix GeneChip Human Mapping Arrays (10K, 100K, 500K, 5.0, 6.0) and associated library and annotation (marker map) files for SNP and copy number analysis.
Below tips and commonly needed files that will help you get the most from your Affymetrix data.
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.
- For Affy 5.0 click the following link: www.goldenhelix.com/download/bin/AffyLibraryFiles_5full.zip
- For Affy 6.0 click the following link: www.goldenhelix.com/download/bin/AffyLibraryFiles_6full.zip
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