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
>
>
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