I'm working on TCGA's data. As we know, we can get '_expression_rsem_isoforms_normalized.txt', '_expression_rsem_isoforms.txt', '_expression_rsem_gene_normalized.txt', '_expression_rsem_gene.txt' of a sample from the RNASeqV2. I have these question:
- Which file should I use to calculate the DEG(differentially expressed gene)? I thought it's '_expression_rsem_gene_normalized.txt'. Is it right?
So if I wanna to get the DEG from the RNASeqV2 data, which tool/method should I use to get? Is t.test applicable for the analysis?
Thanks in advance!