[BioC] Analyzing technical replicates with DESeq2

[Michael Muratet]

Hi Simon

I've been using DESeq2 to analyze RNA-seq data I was given for a multi-factor experiment, three factors with two, three and three levels each with three 'replicates' in each cell. I recently learned that the replicates are actually technical, not biological, and I'm looking for the best way to set up the design matrix to take the correlation into account. 

I don't see anything in the manual or on the list, I'd appreciate your input. Should I use a weighting scheme via normalization factors?

Thanks

Mike


Michael Muratet, Ph.D.
Senior Scientist
HudsonAlpha Institute for Biotechnology
mmuratet at hudsonalpha.org
(256) 327-0473 (p)
(256) 327-0966 (f)

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Huntsville, Alabama 35806