Beta-matrix. Differential methylation analysis
Entering edit mode
21 months 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 • 508 views
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.


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