Thanks Gordon!
I will give it a try.
Sam.
> Date: Tue, 13 May 2014 17:32:59 +1000
> From: smyth@wehi.EDU.AU
> To: genome1976@hotmail.com
> CC: bioconductor@r-project.org
> Subject: limma all by all
> 
> Dear Sam,
> 
> Yes, you can test any comparison.
> 
> > Date: Sun, 11 May 2014 20:53:41 -0400
> > From: somnath bandyopadhyay <genome1976@hotmail.com>
> > Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
> > Subject: [BioC] limma all by all
> >
> > Hi,
> 
> > I have microarray data from 10 different cell types. I want to identify 
> > DEGs by an all cell type by all cell type comparison
> 
> Perhaps just do an F-test.  There are examples of this in the limma User's 
> Guide.
> 
> > and one cell type vs. all cell type comparison using limma.
> 
> Just compute the contrast of one cell type versus the average of the rest. 
> This is usually done with makeContrast() and contrast.fit().
> 
> Gordon
> 
> 
> > Is there a way to do it?
> > Thanks,Sam.
> 
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