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!