Maybe my questions are really easy to some experts, but as a new to TCGA data, I indeed feel confused. So if anyone could give me any ideas, I will be appreciated.
I want to do some analysis on the TCGA level-3 DNA methylation data from various cancer types. However, my question is that, did all the cancer types use the same preprocessing pipeline? And which normalization method did TCGA use? If different cancer types used different preprocessing pipelines, is there any good method to let the comparison among them feasible? Thank you so much.