I'm trying to determine if I can do an unpaired copy number analysis in the Partek Genomics Suite (PGS) v6.6 using .CEL files obtained from CytoScanHD chips (Affymetrix). I am able to download all necessary annotation files, however I cannot find a .cnmodels HapMap file to download, which I need to generate copy number from unpaired samples. PGS v6.6 seems to require a .cnmodels file to do this and does not accept other HapMap reference files like .REF_MODEL. I have previously used .cnmodels for SNP6 and 500K arrays in PGS however I cannot find one for CytoScanHD.
I have 2 questions which I am hoping someone can help me with:
1. Does anyone have a link to a .cnmodels HapMap file for CycoScanHD which I could download?
2. Is it possible to use a different HapMap reference file other than .cnmodels to do unpaired copy number analysis in PGS and if so which reference file and how?
For those of you who possibly stumble upon this question I received an answer from Partek Customer Support and decided to post it here as it might be helpful to someone in the future.
For unpaired copy number analysis there is an option to load a Partek distribution baseline rather than loading a pre-existing .cnmodels file. The Partek distribution baseline is actually prepared using HapMap samples and once selected creates a .cnmodels file, which can be used for future unpaired copy number analyses.
Affymetrix also claims that their Cytoscan HD copy number values do not need paired samples, because they use an internal reference to determine copy number. This may explain why there is no .cnmodels file.
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