I downloaded the TCGA data "RNA_Seq_v2_expression_median.txt" from cBioPortal. The profile description is: Expression levels for 20532 genes in 1212 brca cases (RNA Seq V2 RSEM).
Can I use limma to calculate differentially expressed genes from RSEM data (after log2 (rsem+1) normalization)? If not, which is the best method to perform DE genes in this data set?
I usually work with microarray data and I am new to RNAseq.
Cheers all :)