Beta-matrix. Differential methylation analysis
0
0
Entering edit mode
8 weeks ago
windsur ▴ 20

Hello there, I received a file tab-delimited 16266 x 235 of gene ids with their samples. The data values correspond with the beta values of methylation data. I give a shot with the ChAMP R package, but I do have not the phenotype file or anything else. The idea is to classify the samples according to the data values and see how clustering the data, but I am not quite sure if I should normalize the data or whatever

Can someone help me to analyze that? I do not have any idea how I can manage it.

Sorry for the silly question, but I would be really happy if someone can help me.

r analysis methylation differential • 182 views
ADD COMMENT
0
Entering edit mode

Your question is very vague because everything depends on your data. Where does it come from ? How was it processed ? From which platform are the data ? Was it already normalized or not ? (you mentionned "gene ids" but ChAMP is only applicable to Illumina methylation beadchips so you should have CpGs ids). It is essential that we better know about your data.

ADD REPLY

Login before adding your answer.

Traffic: 1768 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6