[BioC] DEXSeq with no biological replicate?

[Simon Anders]

Dear SangChul

On 2012-04-02 17:29, Sang Chul Choi wrote:
> Is there a way to use DEXSeq with no biological replicate? I used
> DESeq as explained in the manual to use data with no biological
> replicate. In the manual of DEXSeq, I could not find a way of using
> data with no biological replicate.

This is intentional. In principle, one could use the same method as we 
use for DESeq, but this is even more unlikely to give useful results in 
a test for differential exon usage than for differential expression.

The purpose of the "blind" function of DESeq is to give a 
bioinformatician who is confronted with a data set with a botched 
experimental design some tool to salvage at least a few minimal results. 
In my opinion, there is very little point in even trying to perform any 
kind of more advanced analyses, like testing for differential exon 
usage, in such a situation.

   Simon