[R] t.test & p-Value

From: Eleni Christodoulou <elenichri_at_gmail.com>
Date: Wed, 05 Mar 2008 14:33:09 +0200


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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