Using t.test() in this case will likely be very slow. A faster alternative would be to use rowttests() from the genefilter package of Bioconductor.
Best, Jim Henrique Dallazuanna wrote: > You can try this: > > cbind(data.sub, p.value=apply(data.sub, 1, function(x)t.test(x)$p.value)) > > On 03/03/2008, Keizer_71 <[EMAIL PROTECTED]> wrote: >> Hi Everyone, >> >> I need some simple help. >> >> Here are my codes >> >> ##########will give me 10000 probesets#################### >> data.sub = data.matrix[order(variableprobe,decreasing=TRUE),][1:10000,] >> dim(data.sub) >> data_output<-write.table(data.sub, file = "c://data_output.csv", sep = ",", >> col.names = NA) >> >> When i export to excel, it shows me this. This is just a short version. >> There are 1000 rows and 140 columns >> >> Sample_1_D Sample_1_C Sample_2_D Sample_2_C >> 1 2.425509867 11.34031409 11.46868531 11.75741478 >> >> >> Here is my question: How do create a new row and calculate the t-test so >> that it will give me the p-value >> >> Here is what i am looking for. The p-value is not correct but just an >> example. It needs to calculate the entire each row. There are 10000 rows and >> 140 columns. >> >> thanks >> Kei >> >> Sample_1_D Sample_1_C Sample_2_D Sample_2_C p-value >> 1 2.425509867 11.34031409 11.46868531 11.75741478 >> .00341111 >> >> I tried something like this. >> >> t.test(data.sub,mu=0) >> >> I am pretty new to R. I think it is showing me the entire p-value. >> >> >> >> -- >> View this message in context: >> http://www.nabble.com/Calculating-the-t-test-for-each-row-tp15808716p15808716.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. >> > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ______________________________________________ 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.
