I am currently working on to understand the Methylation mechanism in Cancer condition. my area of study revolves around the mostly wet lab and I have basic knowledge about coding, here I need your help. I have two sets of samples from TCGA LUSC and LUAD samples. I want to do Differential methylation analysis between LUSC cancer cells Vs. LUAD cancer cells. Please note I don't want a methylation analysis b/w Normal Vs Tumor. I have tried using TCGAbiolinks but it's not allowing me to choose samples, it's forcing me to have a DME analysis b/w Normal samples VS LUSC or Normal Vs LUAD. Can you please let me know how to solve this issue. Please let me know how to make TCGABiolinks package to understand that I need a comparison b/w samples which I have defined. Sorry for this lengthy post.But trust me this is my last stop. Before I abandon this task.
Thanks in advance, Dave.