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

[jeremy wilson]

Thanks for the reply dear Benilton..

how can then one proceed with QC'ing SNP arrays using BioC?

Considering the quality of arrays are good, does the crlmm algorithm
give good call rates with higher accuracy compared to the Birdseed
algorithm from Affy genome console and the BirdSuit from Broad MIT? I
read in one of your papers
(http://biostatistics.oxfordjournals.org/cgi/content/full/8/2/485)
that the crlmm outperforms other competing algorithms. In the article,
was the crlmm alg compared to DM alg or Birdseed? Does crlmm perform
better even now when compared to the Birdseed?

In my case, how should I do the CNV analysis with only 8 samples. Are
there any other packages or adjustments you can suggest me to
compensate for the small sample size?

Please let me know
Thank you

On Wed, Mar 17, 2010 at 12:17 PM, Benilton Carvalho
<beniltoncarvalho at gmail.com> wrote:
> 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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>