Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Are there any way to find DMR with the data in TCGA methylation level3?
0
gravatar for Makplus T
2.0 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 • 913 views
ADD COMMENT • link •
modified 23 months ago by Kevin Blighe ♦ 65k • written 2.0 years ago by Makplus T • 70

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

ADD REPLY • link written 2.0 years ago by Kevin Blighe ♦ 65k
0
gravatar for Kevin Blighe
23 months ago by
Kevin Blighe ♦ 65k
Kevin Blighe ♦ 65k wrote:

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

Kevin
ADD COMMENT • link written 23 months ago by Kevin Blighe ♦ 65k

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 23 months ago by Makplus T • 70

Great - than you for the follow-up.

ADD REPLY • link written 23 months ago by Kevin Blighe ♦ 65k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 817 users visited in the last hour