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

Benilton Carvalho beniltoncarvalho at gmail.com
Thu Mar 18 11:38:46 CET 2010

Hi Jeremy,

you may want to take a look at:


in summary, crlmm has been compared to BRLMM, BRLMM-P and, more
recently, to Birdseed.

Regarding CNV, we currently don't have anything implemented for small
samples in oligo/crlmm. But Henrik already gave you some
suggestions... ;)


On Wed, Mar 17, 2010 at 8:45 PM, jeremy wilson
<jeremy.wilson88 at gmail.com> wrote:
> 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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