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.
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:
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
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.
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.
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.