Question: Error in methylKit in DMR analysis
gravatar for ahmad mousavi
2.9 years ago by
ahmad mousavi490
Royan Institute, Tehran, Iran
ahmad mousavi490 wrote:


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)
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?


wgbs rrbs • 1.4k views
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