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. Any suggestion will be appreciated! Yiwen He BIMAS/DCB/CIT/NIH

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@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 > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >

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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.