[BioC] TMM normalization of DESeq input data
guest at bioconductor.org
Thu Jun 13 21:18:47 CEST 2013
I have done differential expression analysis over RNA-seq data using both edgeR and DESeq. There are some recently published studies which suggest TMM as the most efficient normalization method (along with DESeq normalization).edgeR already uses TMM. I wanted to ask do you think it is meaningful if I first normalized my raw data using TMM method and send the normalized data to DESeq and of course remove the DESeq normalization commands and then comparing the results obtained from edgeR.
Actually the idea is to have same normalization method for both packages and then comparing the DE results.
Thank you in advance.
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
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