I have 20 (RRBS) samples in 7 groups and it gives below error for clusterSamples: I have got a problem when I run methylkit on Bismark .cov output files, my code :
meth <- unite(myobj, destrand=FALSE) getCorrelation(meth,plot=TRUE) clusterSamples(meth, dist="correlation", method="ward", plot=TRUE)
The "ward" method has been renamed to "ward.D"; note new "ward.D2" Error in hclust(d, HCLUST.METHODS[hclust.method]) : NA/NaN/Inf in foreign function call (arg 11) In addition: Warning message: In cor(t(x), method = METHODS[method]) : the standard deviation is zero
Is there anyone who faced with this problem? or does anybody knows a pipeline for analyzing RRBS data?