DEAR all: i got the test result by such coding et <- exactTest(d, pair=c("c0h","t0h"), dispersion="tagwise") usually should use topTags to adjust the p value, but it canot sort.by gene id or names result <- topTags(et, n=dim(d)[1], adjust.method="BH", sort.by="p.value") i want to use et$table, but donot know how to adjust its p-value thank you very much -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

You don't need topTags() to sort things for you - sorting a matrix or data.frame is a straightforward process. See ?order as well as An Introduction to R. Best, Jim On 9/27/2012 11:46 AM, wang peter wrote: > DEAR all: > i got the test result by such coding > > et<- exactTest(d, pair=c("c0h","t0h"), dispersion="tagwise") > > usually should use topTags to adjust the p value, but it canot sort.by > gene id or names > > result<- topTags(et, n=dim(d)[1], adjust.method="BH", sort.by="p.value") > > i want to use et$table, but donot know how to adjust its p-value > > thank you very much > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099