Question: how to combine sva with survival analysis to validate genes in an independent dataset?
gravatar for a.e.c
2.4 years ago by
a.e.c30 wrote:

dear all,

I have an RNA-seq cancer dataset for which I applied regularized Cox Regression for survival analysis ('Coxnet' from the 'glmnet' R package) obtaining 20 genes associated with survival (genes with coefficients>0). Now I would like to validate these genes with an independent dataset from TCGA but there is a strong batch effect between both datasets due to different library protocols (total RNA with ribo-depletion vs poly-A selection). My idea is to apply surrogate variable analysis to correct for unwanted variation but I need some help on how to proceed. How can I combine a survival analysis with 'sva'? For the validation should I use 'Coxnet' or 'coxph' from the 'survival' R package?

Thanks for your advice,

rna-seq survival coxnet sva coxph • 511 views
ADD COMMENTlink written 2.4 years ago by a.e.c30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1863 users visited in the last hour