I have download GTEX data and TCGA data (only tumor samples available) for a given cancer type using the "recount" R package. After having filtered the genes that are in common between the 2 datasets, I would like to do a differential expression analysis normal vs. tumor.
My question is the following: should I do a kind of "batch" correction to make the comparison meaningful (if so, which tool would you suggest ?) ? or as the data have been processed in a same way by recount I can directly make a comparison ?
how would you proceed ?
NB: I am aware of the https://github.com/mskcc/RNAseqDB database but no data are provided there for my cancer type of interest...
Hope you could help !