DMRcate cpg.annotate error: "Error in data.frame"
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Last seen 6.7 years ago
Sweden

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.

dmrcate • 1.4k views
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Tim Peters ▴ 120
@tim-peters-7579
Last seen 10 months ago
Australia

Hi Pär,

If you remove the 65 SNP probes (rownames starting with 'rs') from the matrix you should be fine.

Best,

Tim

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Last seen 6.7 years ago
Sweden

Super! Thanks for a quick reply!

//Pär

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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

Please have a look to my pipeline.

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Hello,

Best,

Tim

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Hi Tim,

I have given a reply to your post. Could you please check it and let me know. Thank you