Hi,
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!
Kind regards,
Pär
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.
Hi,
I got the same error for my data. I am working with EPIC data. As Tim said I removed the SNP probes but still I am getting the error. Can you please help me in this? Thank you in Advance.
PS. I also made a post at
https://groups.google.com/d/msg/epigenomicsforum/G3yO92pEqzQ/z-KIDzRMBwAJ
Please have a look to my pipeline.
Hello,
I've answered your question in the google groups thread.
Best,
Tim
Hi Tim,
I have given a reply to your post. Could you please check it and let me know. Thank you