Question: how to analysis after get methylation matrix for 850K array?
gravatar for Shaway
10 months ago by
Shaway0 wrote:

Hello everyone,

I'm doing some analysis on 850K data. I have downloaded data from GSE110555.

It's every nice that I found a matrix file from GSE110555, the data format like bellow.

ID_REF R01C01_U R01C01_M R01C01_Pval R03C01_U R03C01_M R03C01_Pval

cg00012701 5853 396 0 6781 582 0

cg00019576 228 12808 0 359 14697 0

Every sample has 3 columns, the 1st is Unmethylated signal, 2nd is Methylated signal and 3rd is Detection Pval.

Here I have three questions.

  1. For computing methylation level, I just using beta value formula M/(U+M+100) for single locus and regions, is it right?
  2. How to find DMR based on this matrix? I can analysis WGBS based on R package bsseq, but it cannot be used for 850K data.
  3. How to link ID_REF(the first column above, like cg00012701) and genome position?

Thank you very much!

ADD COMMENTlink modified 10 months ago • written 10 months ago by Shaway0
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