R help - Feb 2009 - How to avoid losing a sample as reference running an individual differential expression analysis (LIMMA)

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?

Many thanks in advance,
Dmitriy



      
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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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