I believe that the simplest way to deal with technical replicates is to
simply add their counts together, so that you have one column for each
biological replicate.

On Wednesday, May 1, 2013, Michael Muratet wrote:

> 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@hudsonalpha.org <javascript:;>
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
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