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Question: Are there any way to find DMR with the data in TCGA methylation level3?
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gravatar for Makplus T
2.3 years ago by
Makplus T • 70
Makplus T • 70 wrote:

Hi dear all, after downloaded the illumina 450K methylation chip data from TCGA, I have identified the DMCs with Fisher test for each probe, but I have no idea to identify the DMRs. For example I wanna find out the different methy- regions with 1Kb long. Any tool can do it directly? Could any one share some ideas with me? Thanks a lot
dmr methylation tcga 450k • 1.0k views
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modified 2.2 years ago by Kevin Blighe ♦ 69k • written 2.3 years ago by Makplus T • 70

Please see this previous thread: Dmr (Differentially Methylated Regions) Identification Software

ADD REPLY • link written 2.3 years ago by Kevin Blighe ♦ 69k
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gravatar for Kevin Blighe
2.2 years ago by
Kevin Blighe ♦ 69k
Republic of Ireland
Kevin Blighe ♦ 69k wrote:

Take a look at TCGAbiolinks, which provides functionality for this.

Kevin
ADD COMMENT • link written 2.2 years ago by Kevin Blighe ♦ 69k

Thanks for your help. I have finally solved this problem, but what I use is the other tool called ChAMP., it can accept the beta value matrix as input. AND for the TCGAbiolinks, I have noticed it have this function, but when I read its code in GitHub, it seems do the same works for DMRs just as for the DMCs. Maybe I have some misunderstand for that, but finally I choose the other tool, and solve my problem. Thanks again.

ADD REPLY • link written 2.2 years ago by Makplus T • 70

Great - than you for the follow-up.

ADD REPLY • link written 2.2 years ago by Kevin Blighe ♦ 69k
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