[BioC] limma output

James W. MacDonald jmacdon at med.umich.edu
Wed Jun 28 19:04:56 CEST 2006

Hi Stephanie,

stephanie walter wrote:
> Hello,
> 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 
> expression? 

No, you are not correct. The p.value is the p-value associated with a 
particular contrast, whereas the F.p.value is the p-value associated 
with the F-statistic which tests for a difference in _any_ of the factor 


> Thank you very much, 
> Stephanie Walter
> ==================================
> University College Dublin
> College of Life Sciences
> Belfield
> Dublin 4
> Ireland
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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