[BioC] Analyzing technical replicates with DESeq2

[Simon Anders]

On 01/05/13 20:25, Ryan Thompson wrote:
> 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:
>     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.

Ryan is correct: adding up the technical replicates is the way to go. As 
your design is two-way, you will (hopefully) still have enough degrees 
of freedom left to estimate the dispersion.

   Simon