TCGA survival analysis using >100 genes

Question

[veronico]

Hi everyone,

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.

Thank you!

[Shicheng Guo]

With R loop, you can make 60,000 survival analysis for each RNA-seq gene.

[Ram]

Skip loops, use apply instead.

[veronico]

Ok, thank you. I'll look into apply

[veronico]

for each gene? My apologies I am not following. Would this work if I have a panel of a >100 genes that I want to investigate together?

[Shicheng Guo]

Sure. I think you should make a better definition for. What exactly you want to do. "do survival analysis by using a panel of >100 genes" is not so clear.