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SNP, ROH and CNV Association Analysis Overview with Affymetrix SNP Arrays 5.0 and 6.0

Library Files

For mapping arrays prior to to the SNP 5.0 and SNP 6.0 arrays, you must have the corresponding library file installed for each type of mapping array you want to import. SNP 5.0 and 6.0 mapping arrays do not require library files. If you have GCOS installed, it is likely the library files are already installed in either C:/GeneChip/Library or C:/GeneChip/Affy_Data/Library.

For non-GCOS users HelixTree now supports the direct download of Affymetrix Library files from Affymetrix through the NetAffx service. See section 4.3.6.3 of the latest HelixTree manual for importing library files through NetAffx.

Marker Maps/Annotation Files

The latest SNP marker maps/annotation files can be downloaded directly using Affymetrix NetAffx included within HelixTree. See section 4.3.5.3 of the latest HelixTree manual for importing annotation files through NetAffx.

Affymetrix 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. Here they are:

http://www.goldenhelix.com/download/bin/500kCaseControlResponse.ghd.zip (48 patients)
http://www.goldenhelix.com/download/bin/500kContinousResponse.ghd.zip (48 patients)
http://www.goldenhelix.com/download/bin/100kCaseControlResponse.ghd.zip (90 patients)
http://www.goldenhelix.com/download/bin/CaseControl2880Patients100k.ghd.zip (2880 patients)
http://www.goldenhelix.com/download/bin/100kContinousResponse.ghd.zip (90 patients)

Once they are UNZIPPED, they will appear as a .ghd file on your computer. These files can only be opened within HelixTree. From the project window select >File >Import Data >Import legacy GHD file.

If you are interested in importing raw Affymetrix .chp files using HelixTree, feel free to download the following files:

http://www.goldenhelix.com/download/bin/50KhindCHPFiles.zip
http://www.goldenhelix.com/download/bin/50KxbaCHPFiles.zip
http://www.goldenhelix.com/download/bin/250KnspCHPFiles.zip
http://www.goldenhelix.com/download/bin/250KstyCHPFiles.zip

The above .chp files can also be downloaded from the Affymetrix website. However, you will need to process the data to extract the .chp files yourself.

http://www.affymetrix.com/support/technical/sample_data/500k_data.affx
http://www.affymetrix.com/support/technical/sample_data/hapmap_trio_data.affx