Which Platform And Batches Should I Select From Tcga For My Study?

Question

[jack]

I want to get data from TCGA to build a gene regulatory network for one of the cancer. I have a few questions out of it:

1) Should I select one type of Center/Platform for getting data? 2) What is the different batches of data? Is it recommended to have all baches of my data from one type of cancer for gene regulatory network reconstruction?

Answer 1

[Charles Warden]

Each data type is typically produced from a single center. In most cases, you can find different types of data for a single patient, but each data type comes from somewhere else. Nevertheless, I think this is probably OK.

"gene regulatory network" is kind of a broad term. There are lots of ways to build gene regulatory networks, so I think you would have to describe a particular algorithm to get more detailed feedback. That said, I wouldn't consider it trivial to determine the run-dates within say RNA-Seq data (perhaps that information is somewhere in the metadata, but I have not personally found and used that information), so I think you should get downloading all available data for whatever you are trying to analyze.