[BioC] Limma: Extract genes from decideTests result

[John Fernandes]

This isn't elegant but should give you the genes you want:

    pattern <- c(1,1,0)
    fit$genes[results[,1]==pattern[1] & results[,2]==pattern[2] &
results[,3]==pattern[3],]

----- Original Message -----
From: "James W. MacDonald" <jmacdon at med.umich.edu>
To: "He, Yiwen (NIH/CIT) [C]" <heyiwen at mail.nih.gov>
Cc: <bioconductor at stat.math.ethz.ch>
Sent: Friday, March 03, 2006 4:32 PM
Subject: Re: [BioC] Limma: Extract genes from decideTests result


> 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".
>
> HTH,
>
> Jim
> >
> > Any suggestion will be appreciated!
> >
> > Yiwen He
> > BIMAS/DCB/CIT/NIH
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> --
> James W. MacDonald
> University of Michigan
> Affymetrix and cDNA Microarray Core
> 1500 E Medical Center Drive
> Ann Arbor MI 48109
> 734-647-5623
>
>
>
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