Hi, I managed to get "dataDEGs" for miRNAs from TCGA-PRAD database using TCGAbiolinks. I also downloaded clinical data from the TCGA. How can I introduce a "clinical.info=radiation" factor to see radiation induced DE miRNAs ?
clinical.radiation <- GDCprepare_clinic(query, clinical.info = "radiation") datatable(clinical.radiation, options = list(scrollX = TRUE, keys = TRUE), rownames = FALSE)
Also, how to measure "Survival" among patients with and without radiation (for selected DE miRNAs) ?
Is it better to use "legacy" or "harmonized" data for miRNAs for above analysis. Is "harmonized" data already normalized for counts.