[BioC] EdgeR 'average' cpm

[Gordon K Smyth]

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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