[BioC] limma output

stephanie walter stephanie.walter at ucd.ie
Tue Jun 27 13:46:16 CEST 2006


I'm using limma to normalize and analyse two colour dye swap arrays. 
In the output file I am getting two different p values:
I. p.value
II. F.p.value
I attached an example of the command file I'm using.
I suppose the first p value (p.value) is the raw p value and the 
second (F.p.value) is the p value adjusted with the FDR value. Can you 
please tell me if this assumption is correct and if it is correct to 
use this F.p.value to make conclusions on differential gene 

Thank you very much, 
Stephanie Walter

University College Dublin
College of Life Sciences
Dublin 4
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