[BioC] log2 as input in limma

James W. MacDonald jmacdon at uw.edu
Fri Sep 12 15:24:50 CEST 2014

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.



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.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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