[R] clustering based on most significant pvalues does not separate the groups!

[pguilha]

Hi all,

I have some microarray data on 40 samples that fall into two groups. I have
a value for 480k probes for each of those samples. I performed a t test
(rowttests) on each row(giving the indices of the columns for each group)
then used p.adjust() to adjust the pvalues for the number of tests
performed. I then selected only the probes with adj-p.value<=0.05. I end up
with roughly 2000 probes to do the clustering on but using pvclust, and
hclust, the samples do no split up into the two groups. I would have
imagined that using only those values that are significantly different
between the two groups, the clustering should surely reflect that?

Please, what am I missing!!!!???

Thanks!

Paul

PS: I am hoping I have just thought this through in the wrong way and there
is a simple explanation, but can provide the code I am using for clustering
if necessary!



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