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Question: log2 as input in limma
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3.2 years ago by
Guest User12k
Guest User12k 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.
ADD COMMENTlink modified 3.2 years ago by James W. MacDonald45k • written 3.2 years ago by Guest User12k

Can you provide details of the batch normalization you did? 

It might (likely) be better to include the batches as covariates in a design matrix, and shoot that design matrix along with the raw count data through `limma::voom`

ADD REPLYlink written 3.2 years ago by Steve Lianoglou12k
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3.2 years ago by
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James W. MacDonald45k wrote:
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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]
ADD COMMENTlink written 3.2 years ago by James W. MacDonald45k
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