atakanekiz
commented
6 years ago Hi Jason,
Were you able to solve this issue. I think I'd like to employ a similar approach and I'm running into problems. You can see my post here: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/225
From a cancer microarray dataset analysis, i have identified a small gene signature, which i would like to validate further through RNA-Seq data and TCGAbiolinks. However, i wondered for one further scenario that i would like to test if feasible through TCGAbiolinks:
based on a specific dataset of interest-which is TCGA-COAD-, is it possible to perform a survival analysis for these specific genes ? To inspect for any significant associations ?
I found the specific section in the tutorial (https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/tcgaBiolinks.html#tcgaanalyze_survival:_survival_analysis:_cox_regression_and_dnet_package) regarding Survival analysis
Thus:
1) I should proceed similarly, or if i have already download raw HTSEQ counts and all clinical data, i should only normalize them ?
2) Is it then possible to subset to only for these specific genes of interest somehow in the function _TCGAanalyzeSurvivalKM ?
Thank you in advance and please excuse me for my naive question, but i have never performed a survival analysis before!!