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

[Benilton Carvalho]

Hi Jeremy,

currently there isn't anything like arrayQualityMetrics implemented in
oligo/crlmm.

About the sample size, you need at least 10 samples to use
crlmm::computeCopynumber.

b

On Wed, Mar 17, 2010 at 4:45 PM, jeremy wilson
<jeremy.wilson88 at gmail.com> wrote:
> 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
>
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