hi, I currently downloaded the data_RNA_Seq_v2_expression_median.txt from cbioportal. I found the read_counts is not integer and I don't know how to process this type of normalized data with Deseq2.
Should I download the previous-leveled data from portal and use Deseq2 from bottom to the top, or is there other package to find out the differentially expressed genes?
Hugo_Symbol TCGA-BJ-A0YZ-01 TCGA-BJ-A0Z0-01 TCGA-BJ-A0Z2-01 UBE2Q2P2 1.8867 2.6927 10.0867 HMGB1P1 139.6335 181.2141 203.7297 LOC155060 45.3978 131.8725 248.4856 RNU12-2P 0.4165 0.3948 0.9502 SSX9 0 0 0 CXORF67 0 1.1845 2.3756
Hope some with experience handling the pre-processed data from TCGA could answer this question.