DMRcate cpg.annotate error: "Error in data.frame"
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@parlarsson-9314
Last seen 5.4 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 • 1.1k views
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Tim Peters ▴ 120
@tim-peters-7579
Last seen 6 weeks ago
Australia

Hi Pär,

It looks like the same issue another user had earlier in that thread. https://groups.google.com/d/msg/epigenomicsforum/GTqdjzRoI08/GGY-Ju4FwHMJ

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

 

Best,

Tim

 

 

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@parlarsson-9314
Last seen 5.4 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

https://groups.google.com/d/msg/epigenomicsforum/G3yO92pEqzQ/z-KIDzRMBwAJ

Please have a look to my pipeline.

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Hello,

I've answered your question in the google groups thread.

 

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

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