[BioC] topTable gene list

daphne mouzaki (RI) daphne.mouzaki at bbsrc.ac.uk
Wed Sep 13 16:13:01 CEST 2006


hi,

I have generated a list of significant genes for 3 time points
separately using the function
"decideTests"in Limma package.Using this function I generated
foldchanges and FDR for every
gene using method Benjamini and Hochberg ("BH") and p.value=0.05. 
I was wondering if it is possible to generate all the FDR and
foldchanges with the respective 
gene name for every time point. 
I tried changing the cut-off to 1 in order not to exclude anything and
the method set to the 
function "decideTests" changed to "none" but it doesn't work. 
Could you recommend any other possible ways?

I would appreciate any help,

Daphne



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