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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 Timze W
14 months ago by
Timze W • 40
Timze W • 40 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 • 634 views
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modified 12 months ago by Kevin Blighe ♦ 51k • written 14 months ago by Timze W • 40

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

ADD REPLY • link written 14 months ago by Kevin Blighe ♦ 51k
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gravatar for Kevin Blighe
12 months ago by
Kevin Blighe ♦ 51k
Kevin Blighe ♦ 51k wrote:

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

Kevin
ADD COMMENT • link written 12 months ago by Kevin Blighe ♦ 51k

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 12 months ago by Timze W • 40

Great - than you for the follow-up.

ADD REPLY • link written 12 months ago by Kevin Blighe ♦ 51k
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