How to use DNAcopy package to analyze Affymetrix SNP array?

Question

[Shixiang]

Hello,

I find TCGA project using DNAcopy to analyze their SNP6.0 data, so I wanna use this package to preprocess Affymetrix SNP array (CEL files) downloaded from GEO database like them. I am confused that DNAcopy documentation tells that it is used to analyze CGH data, and how can it apply to SNP array? There are little information from google search can help me use this package for SNP array (the DNAcopy documentation use CGH data as input).

My key point is that how can I preprocess Affymetrix SNP array for copy number analysis and use CBS to segment.

Thanks.

Answer 1

[Eric T.]

You might have better luck with the PSCBS package, which wraps DNAcopy and includes more functionality (and documentation) for processing SNP data.