[BioC] topTable gene list

[James W. MacDonald]

daphne mouzaki (RI) wrote:
> 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. 

If you want everything then decideTests() is probably not the function 
you want. Instead, you should try topTable(). Something like this should 
work:

topTable(<MArrayLM object>, coef = 1, number = <number of genes on chip>)

You can then change 'coef' to 2, 3,... depending on the number of 
contrasts you have.

HTH,

Jim

> 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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-- 
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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