[BioC] SNP Analysis

Vincent Carey stvjc at channing.harvard.edu
Wed Oct 21 16:11:59 CEST 2009

Briefly, you can perform genotype calling with a confidence measure
using crlmm package, working from the CEL files.   The crlmm package
includes a vignette called crlmmDownstream.pdf that illustrates one
approach to GWAS analysis based on 6.0, using snpMatrix package.  To
use crlmm you will also need a metadata package called

There are certainly other approaches possible.  Our workflow
documentation for this use case probably needs some enhancement.

On Wed, Oct 21, 2009 at 9:42 AM, Peter Ganske <Peter.Ganske at hki-jena.de> wrote:
> Hello,
> first time for me to work with SNP arrays. I got CEL- and CHP-files for my Analysis. The CEL are from Affymetrix Human-Wide Genome SNP- Array 6.0 and the CHP- files are dealed with the Birdseed- Algorithm (part of the Genotyp Console from Affymetrix as well).
> Is there anybody here, who worked with this arrays in the past? I am looking for an (general) workflow for my study. I want to analyse patients with Rheumatoid Arthritis with regard to SNPs and the question "why there are respoonder and non-responder for the therapy"?
> I am looking for an workflow for the arrays. Is it better to work with the CHP files or with the CEL- files?
> Would me great, if anybody can help me out.
> Thanks in advance
> Peter
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