[BioC] log2 as input in limma

[James W. MacDonald]

If you want to use count data in limma, you should use the voom function,
which not only converts to log cpm, but also computes observational-level
weights that can then be used as part of the modeling process.

See ?voom and the limma User's Guide for more information.

Best,

Jim



On Fri, Sep 12, 2014 at 3:31 AM, R [guest] <guest at bioconductor.org> wrote:

> Hi all,
> I have performed batch-normalization on my RNA-Seq data leaving the data
> as cpm-log2 normalized. How do I use this as input in limma? It usually
> only take count data.
>
>  -- output of sessionInfo():
>
> none
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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