[BioC] DESeq and number of replicates required for RNA-Seq

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Mon Jun 14 15:45:58 CEST 2010


This follows on slightly from my experimental design thread.

Having worked through the vignette for DESeq, it seems to work well.  However, for the TagSeqExample.tab data set, when using an FDR cut off of 0.05, what we see is that we only find differential expression for large fold changes - an average of log2 fold change of 5 for up-regulated, and log2 fold change of -5 for down-regulated.  There are very few significant results that even go as far down as 2 or -2 - which is still a 4-fold change.

So, the question is, how many replicates must we have to get more sensitive results?  Say down to log2FC of 1? (two-fold up or down regulated)?

I can calculate this by using DESeq's own estimates of variance to approximate replicates for T and N in the example data, and keep going until my significant results start to hit a logFC of 1, but I wanted to know if anyone else had done this yet?


More information about the Bioconductor mailing list