I have downloaded TCGA Breast cancer normalised data sets from 1000 samples form RNA seq V2 . The counts files have only two columns such as Gene_id and Normalised Counts.
gene_id normalized_count 100130426 11.691 10357 114.6254
My goal is to do Differential expression analysis among these datasets, with various other clinical conditions such as Age, treated/untreated etc.
Please let me know whats the best possible way to do it. or is it possible to do DGE analysis with various clinical parameters?
Your suggestions is highly valuable. Thanks a lot for your help.