I am looking to perform differential analysis for an experiment with a relatively unusual design.
We have RNA-seq for 60 disease and control samples and would like to conduct differential analysis between the conditions. These samples were generated in 8 separate iPSC differentiation batches, and it would not be surprising to have significant batch effects between batches. Our idea was to include a technical replicate in each of the 8 batches which would give us a sense of the variance among batches.
I've already tried including including batch as a blocking factor in DESEQ/EDGER, but this approach does not take advantage of the replicate in each batch. So my questions are
- Can DESEQ/EDGER accommodate such an experimental design?
- If not, are there others that might help?