[BioC] EdgeR 'average' cpm

Gordon K Smyth smyth at wehi.EDU.AU
Sun Apr 14 11:14:28 CEST 2013


Dear AEC,

You could get average cpm for each group in several ways.  You could 
subset the DGEList by group and compute aveLogCPM() on each subset.  Or 
you could fit a linear model with a coefficient for each group, then the 
fit$coefficients hold the aveLogCPM for each group.

Best wishes
Gordon

---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
http://www.statsci.org/smyth

On Fri, 5 Apr 2013, Anna Esteve Codina wrote:

> Dear all,
>
> I am a edgeR user and I would like to know if edgeR reports 'average' cpm
> for each of the conditions tested in the analysis. Having a look at the
> output it seems the only information I have is the 'average' log(cpm)
> calculated using all the libraries. So the question would be, is there any
> way to output 'average' cpm (condition 1) and 'average' cpm (condition 2)
> for each tag ?
>
> Thanks for clarifying me this point.
>
> AEC.
>
>

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