[BioC] QC Affy 6.0 SNP arrays with crlmm or Oligo?

[jeremy wilson]

Dear all,

I am wondering if there is a QC methodology like the "contrast QC"
check by the affymetrix genome console to QC the arrays before
genotyping. The crlmm and Oligo packages do the normalization and
summarization which is awesome but I do not see it doing QC checks. I
am trying to see the quality of the chips with nice plots similar to
that of from "arrayQualityMetrics" package for gene expression arrays.

One more question: I have only 8 arrays from the same lab and I need
to do LOH and copy number analysis. Will the small number of arrays be
problematic?

Awaiting for your reply,
Thank you
JW