Hello,

When running DESeq2, I have some data and some genes with VERY low-pvalues (e.g. 3.12077x10^-8) were being filtered out with independent filtering, I looked more into it and found something that seems unusual.  I looked at the filtering cutoffs and they mostly low with one exception: 

5.837401
->>> 165.6933
5.837401
5.837401
5.837401
15.20571
41.06299
5.837401
2.722993
41.06299

There is one cutoff 165.69 which seems extremely high.  How can I figure out why that is???  I have been going through the manual and was about to try to illustrate for myself the BH procedure but I was wondering if that's the right approach.  Thanks in advance very much,

Ramiro

Ramiro

thanks for enquiring. It will be difficult to reply with the information provided. Can you post a self-contained code example and state how exactly the obtained output differs from what you expect?

http://www.bioconductor.org/help/support/posting-guide/

Kind regards

Wolfgang