[BioC] limma all by all

Gordon K Smyth smyth at wehi.EDU.AU
Tue May 13 09:32:59 CEST 2014


Dear Sam,

Yes, you can test any comparison.

> Date: Sun, 11 May 2014 20:53:41 -0400
> From: somnath bandyopadhyay <genome1976 at hotmail.com>
> Cc: "bioconductor at r-project.org" <bioconductor at 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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