[BioC] Results file LIMMA

[James W. MacDonald]

Andres Gutierrez wrote:
> Hello,
> 
> I'm new using LIMMA for the analysis of two color arrays. I have been following
> the user guide but I have questions regarding the meaning of the values and
> columns of the output "results" file.  
> 
> Where can I find an detailed explanation of the output file?, I mean the
> statistical definition of each column: A, Coef., t., p.value, F and Res. I guess
> that since I'm using adjust="fdr" in the code, the p values for each contrast
> are already adjusted for fdr and I can make my own cut (e.g. 5% or 1%) to find
> the MOST significant ones. Am I right?.

The output from topTable is already sorted with the genes most likely to 
be significant at the top, so you can set your cutoff to select genes 
with an FDR less than a certain level.

As for a statistical definition, you might look at the Bioconductor 
Monograph. I thought the Limma User's Manual covered that pretty well too.

Best,

Jim


> 
> Thanks,
> 
> Andres
> Texas A&M University
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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