Calculate t.test for a matrix
On Apr 14, 2012, at 11:40 AM, Junyu Lee wrote:
Hello everyone, I have a data frame (tt), see below (I only show 2 genes, actually I have a lot):
Shouldn't you be working with a statistician to get advice about how to handle the multiple comparison issues you are most certainly facing?
David. > > group gene1 gene2 Control 28.9776 9.9355 > Control 28.9499 10.0997 Control 29.5468 14.2995 Control 29.5246 > 13.9561 > Test1 29.1864 9.7718 Test1 29.2048 10.0388 Test1 34.9563 11.9509 > Test1 > 34.9464 11.8909 Test2 36.9566 14.5316 Test2 37.1309 14.5188 Test2 > 36.1017 > 29.5468 Test2 36.0883 29.5246 > I'd like to calculate p values: Test1 vs Control and Test2 vs Control > respectively for Gene1. Similar calculate performed for Gene2. > > I tried: > > sapply(levels(fac), function(x) t.test(tt1$gene1, > tt$gene1[which(fac==x)])$p.value) # I don't really understand how it > works, I copied from genefilter. > > where: fac=as.factor(tt$group) > > It seemed to work for first column. I don't know how to use apply() > to > make it work on rest of column because I used tt$gene1 specifically. > Or > whatever method that works > > Thank you in advance. > > Junyu > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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. David Winsemius, MD West Hartford, CT