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")$p.value)
}
which(p.values<0.01)
where Significant is my matrix of genes and their expression in tumors and
positive, negative are subsets of thes matrix.
Whn p<0.01, I reject the null hypothesis and I accept the alternative one,
that I have greater gene expression in positive than in negative.
I assume I must be doing sth wrong because the heatmap that I get with the
genes that pass the filter of p-value is wrong.
Could anyone help me with this?
thanks a lot,
Eleni
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I am sorry, the test is unpaired...But my question remains Thanks, Eleni On Wed, Mar 5, 2008 at 2:33 PM, Eleni Christodoulou <elenichri@gmail.com> wrote:> Hello list, > > I am trying to apply the paired t.test between diseased and not diseased > patients to identify genes that are more expressed in the one situation > under the other. In order to retrieve the genes that are more expressed in > the positive disease state I do: > p.values<-c() > for(i in 1:length(Significant[,1])){ > p.values[i]<-try(t.test(positive[i,],negative[i,],alternative > ="greater")$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]]
On Wed, Mar 5, 2008 at 2:05 PM, ian white <i.m.s.white@ed.ac.uk> 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 <elenichri@gmail.com > > > > 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 > > stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > >[[alternative HTML version deleted]]