Beta-matrix. Differential methylation analysis
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.
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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.