Entering edit mode
10 months ago
Gnana
•
0
To perform survival analysis for normal vs tumor cancer sample what kind of rna seq data is to used?
- unstranded
- stranded_first
- stranded_second
- tpm_unstrand
- fpkm_unstrand
- fpkm_uq_unstrand
Which of these shoud be used and is there any normalisation to be done?
Survival analysis tumor vs normal? I can already tell you that normal survives longer than tumor. Please add some details what exactly you want to do because the question as by now makes no sense.
I want to check the survival for a specific gene in normal vs tumor condition in Tcga data.
What do you mean by "survival of a gene"?
Your first question - use GDCquery - it takes care of loading the expression data:
Yes normalisation is required:
Follow up on ATpoints comment because he is 100% correct:
Take a look at GEPIA: http://gepia.cancer-pku.cn/index.html to look at survival plots for a single gene in a TCGA dataset
In GEPIA, the two lines in the kaplan-meier plot represent patients stratified into two groups using median gene expression cutoff... each group containing normal and tumor samples...