[BioC] prefiltering genelist before LIMMA & cut-off paramter for getting DEGs from topT object.

deb [guest] guest at bioconductor.org
Fri Dec 6 09:16:51 CET 2013

Dear all,

I am grateful to you for the prompt reply to my query.

1) So I think adj.p.value with "BH" adjust.method (which also takes " FDR" issues into consideration) will be my choice for extracting significant DEGs.
But I am looking into the propnulltrue function also to get more ideas.

2) I do however need some ideas on your suggestion regarding "If you want to give even more priority to larger fold changes, then we recommend that you use treat().  This is better than just cutting on estimated logFC

Can you please enlighten me on the issue?

3) I have one more question regarding the utility of genefilter() in
pre-filtering normalised data based on mean expression intensity prior to
LIMMA. I all advisable examples filtering has been done for minimum
expression intensity as 3.5 and follow-up statistics is multtest,SAM or
t-test with multiple adjustment. Do you recommend to do it before LIMMA?

Thanks in advance for your suggestions.


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