Message-ID: <6phr627nfs5.fsf@gopher4.fhcrc.org>
Date: 2009-02-10T03:15:38Z
From: Martin Morgan
Subject: How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)
In-Reply-To: <494240.40561.qm@web111514.mail.gq1.yahoo.com> (Dmitriy Verkhoturov's message of "Mon, 9 Feb 2009 10:22:52 -0800 (PST)")
Dmitriy Verkhoturov <verkhoturovdm at yahoo.com> writes:
> Hello listmemebers,
>
> I have data from two-color microarray expression profiling experiments
> where 3 whole brain (WB) samples were compared to 3 Mauthner Cells
> (MC) in a loop design (-> MC #1 -> WB #1 -> MC #2 -> WB #2 -> MC #3 ->
> WB #3 -> MC #1 ->). In addition to phenotype analysis I would also
> like to run an individual analysis making all pair-wise
> comparisons. I'm using the LIMMA package in R to do this. The problem
> is that the contrast matrix that you have to set up requires that one
> of the samples be designated as a reference, but in doing so you lose
> the sample. My question is this, is it possible to run individual
> analysis with this data set without losing one as a reference point?
Hi Dmitriy --
Please ask Bioconductor questions on the Bioconductor mailing list.
http://bioconductor.org/docs/mailList.html
Best,
Martin
> Many thanks in advance, Dmitriy
>
>
>
>
> [[alternative HTML version deleted]]
>
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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