Hello,

I retrieved the expression data for 290 samples (divided in two groups based on treatment result from the clinical data) for TCGA-BRCA project and performed their differential expression analysis. Now i want to check for the methylation status for only those selected samples. But when i downloaded the methylation data of all samples of TCGA-BRCA, none of the samples matched with my selected 290 samples.

Is it the right way to do the methylation analysis? Or TCGA sample barcode varies for expression and methylation data. Same happens when i performed mutation analysis on those selected samples none of them matches with the maf matrix of all TCGA-BRCA mutation data.

Please give some insight into this. I'm really stuck in my studies.