Hi, I am relatively new to R and Bioconductor and am trying to filter the topTable that I generated of differentially expressed genes from my normlized eset file comprised of ~ 40 HG-133A Affy microarrays . I would like to see if particular probesets are represented in this list. Alternatively I would like to generate a topTable of differentially expressed genes using only specified probesets within my eset file.
Can anyone tell me how I would begin to approach this? I have looked into using the genefilter() function but can't figure out if it can take the right parameters (i.e. specific probe set id's). Thanks in advance, -M This is the code I used to generate my topTable > fit <- lmFit(eset, design) > cont.matrix <- makeContrasts(NormalvsTumor=Tumor-Normal, levels=design) > fit2 <- contrasts.fit(fit, cont.matrix) > fit2 <- eBayes(fit2) > topTable(fit2, number=100, adjust="BH") -- View this message in context: http://r.789695.n4.nabble.com/filtering-probesets-with-Bioconductor-tp4097747p4097747.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
