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! -- View this message in context: http://r.789695.n4.nabble.com/clustering-based-on-most-significant-pvalues-does-not-separate-the-groups-tp3644249p3644249.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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.
