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.

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]]