I'm having issues DMRcate with my dataset. Using the demo data works fine.
The design was initially a problem, but worked out after following advice here: DMRcate cpg.annotate error .
However, when I get past this it still exists with an error:
> t_ann <- cpg.annotate(TC.M.nSNPs, analysis.type="differential", design=design, coef=2)
Your contrast returned 254877 individually significant probes. We recommend the default setting of pcutoff in dmrcate().
Error in data.frame(ID = rownames(object), weights = weights, CHR = RSanno$chr, :
arguments imply differing number of rows: 438529, 438464
Not sure what's going on here. Any advice is greatly appreciated!
PS. I made a post at https://groups.google.com/forum/#!search/dmrcate$20bioconductor/epigenomicsforum/GTqdjzRoI08/N2YUQajpBAAJ, but I am posting here as well in case the google group does not get read.