I hope everyone is doing well!
I was wondering if anyone knew how to do survival analysis by using a panel of >100 genes? I have a list of genes I am interested in (>100 genes) and I want to find these list of genes that are down regulated from RNA seq data from TCGA (preferably Breast Cancer), please?
I was using this method, that was amazingly made by TriS: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
However, I am unsure on how to 1) find only downregulared genes and 2) do survival analysis pertaining to >100 genes.
My apologies for the newb question. I am new to R. I got TriS' method to work for genes altered, but I am interested in a different question.