[BioC] DESeq/DESeq normalization on different experiments

Gilgi [guest] guest at bioconductor.org
Thu May 22 10:26:55 CEST 2014


Hello,

I have ~100 RNA seq-samples from the same organism, but they include different experiments (each experiment of 6-16 samples). I would like to put all together into our RNA seq pipeline, that includes  mapping, htseq count and DESeq. Differential expression comparisons will be done of course only between samples of a single experiment (due to possible batch effects). However, will it be a good idea to normalize all samples together?
The assumption behind the normalization is that most genes are not differentially expressed, but between different experiments the variability might be higher. Therefore I wanted to ask your opinion on doing the normalization on such a large combined data-set.

Thank you,
Gilgi

 -- output of sessionInfo(): 

none

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