[BioC] Subject: Re: Comparing Two Affymetrix Arrays Question

[Abboud, Ramzi]

Swapna,

Thank you for your reply.

Following your advice I have taken a look at ?genas in limma.  Biologically I am not toaly sure this approach makes more sense in regards to this experiment, but it is something I will discuss with the PI.  Either way I would like to familiarize myself with ?genas, and I have a couple of questions.

The function seems to return correlation between the two data sets as a whole.  Does it do so on a gene by gene basis, (ie is gene X correlated) rather than just the overall correlation?  Would computing a correlation for each gene even make sense statistically?  Right now I can only see overall correlation.

Thank you,
Ramzi
________________________________________
From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Swapna Menon [swapna30 at gmail.com]
Sent: Sunday, June 26, 2011 4:41 AM
To: bioconductor at r-project.org
Subject: [BioC] Subject: Re:  Comparing Two Affymetrix Arrays Question

Hi Ramzi,

>From what I understand about your problem, your question is what is the
difference between group A and B. The answer would be in the contrast A -
wild type vs contrast B -wild type, if wild type is a common control for
both and not in the direct contrast of A-B. If this is your situation, you
may also want to see ?genas in limma.

Best wishes,
Swapna

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