Hi,

I'm completely new to bioinformatics. I was trying to do a differential RNA seq analysis on a TCGA dataset (STAD samples); specifically between specific groups of STAD samples. I downloaded individual TCGA STAD samples as tar.gz files on to my computer. Several questions: 1.) do I need to put these samples into R?; 2.)is there a code that I could plug into R to obtain the differences in RNA in the two sets of STAD samples? 3.) Is DeSeq2 involved in this?

Sorry that these are very basic questions--I have absolutely no computer experience right now.

I suggest you first take some basic tutorials towards R and file imports and them go through the Bioconductor RNA-seq workflow and the DESeq2 vignette. HBC has great tutorials on DESeq2 as well. This will get you started with the concepts so you can answer this question yourself. The purpose of the support site is to help with technical problems, not really to teach the absolute basics, please understand that. Yes, DEseq2 can do the differential analysis for you.