Hi Eleni, Check *"Computing Thousands of Test Statistics Simultaneously in R" *in http://stat-computing.org/newsletter/v181.pdf
Other alternative could be the multtest package. HTH Jorge On Wed, Mar 5, 2008 at 8:55 AM, Eleni Christodoulou <[EMAIL PROTECTED]> wrote: > On Wed, Mar 5, 2008 at 2:05 PM, ian white <[EMAIL PROTECTED]> wrote: > > > Don't you need to make some allowance for multiple testing? E.g. to get > > a experiment-wise significance level of 0.01 you need > > > > which(p.values < very small number) > > > > where the very small number is approximately 0.01/(total number of > > genes). > > > > On Wed, 2008-03-05 at 14:38 +0200, Eleni Christodoulou wrote: > > > I am sorry, the test is unpaired...But my question remains > > > > > > Thanks, > > > Eleni > > > > > > On Wed, Mar 5, 2008 at 2:33 PM, Eleni Christodoulou < > [EMAIL PROTECTED] > > > > > > wrote: > > > > > > > Hello list, > > > > > > > > I am trying to apply the paired t.test between diseased and not > > diseased > > > > patients to identify genes that are more expressed in the one > > situation > > > > under the other. In order to retrieve the genes that are more > > expressed in > > > > the positive disease state I do: > > > > p.values<-c() > > > > for(i in 1:length(Significant[,1])){ > > > > p.values[i]<-try(t.test(positive[i,],negative[i,],alternative > > > > ="greater")$p.value) > > > > } > > > > > > > > which(p.values<0.01) > > > > > > > > > > > > where Significant is my matrix of genes and their expression in > > tumors > > > > and positive, negative are subsets of thes matrix. > > > > Whn p<0.01, I reject the null hypothesis and I accept the > alternative > > one, > > > > that I have greater gene expression in positive than in negative. > > > > I assume I must be doing sth wrong because the heatmap that I get > with > > the > > > > genes that pass the filter of p-value is wrong. > > > > > > > > Could anyone help me with this? > > > > > > > > thanks a lot, > > > > Eleni > > [[alternative HTML version deleted]] ______________________________________________ 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.