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I have just installed ChAMP and all of its dependencies for methylation 450k analysis.

I was trying out the tutorial (http://www.bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.pdf) but got an error.

When running the Probe Lasso DMR Hunter, I encounter "You have found 4161 significant MVPs with a BH adjusted P-value below 0.05 Error in [.data.frame(dmr.beta.means, , 22:24, ) : undefined columns selected"

The error prevents halts the analysis, and I can't replicate what is shown in the above-mentioned tutorial.

I have tried uninstalling and re-installing ChAMP, to no avail...

Any advice and insight will be much appreciated! Thanks in advance!

Jaap
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Nicholas Syn
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1 Answers1

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using R 3.1.0, the error can be solved.

abcd1
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  • Many thanks - indeed, the problem appears to lie with R 3.2.1. I re-installed R 3.1.0, and there's no such problem. – Nicholas Syn Jul 22 '15 at 11:13