[BioC] Limma: Extract genes from decideTests result

James W. MacDonald jmacdon at med.umich.edu
Sat Mar 4 01:32:37 CET 2006

Hi Yiwen,

He, Yiwen (NIH/CIT) [C] wrote:
> Hi, 
> In limma, one can use decideTests to assign each gene up/down/NC coded
> as 1/-1/0, and then use vennCounts to count the number of genes for each
> pattern. My question is, how can one actually extract a list of genes
> with a particular pattern? For example, if I'm looking at 3 contrasts,
> and I want all the genes that are significantly up in the first two but
> no change in the last (1, 1, 0), how should I do it?
> I couldn't make subset work because the resulting object from
> decideTests (class of TestResults) could not be converted into a
> data.frame.

I don't know a clever way to do this, but for an example of a kludgy way 
you could look at the code for vennSelect() in affycoretools, in 
particular the code for method = "sameup".


> Any suggestion will be appreciated!
> Yiwen He
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James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109

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