how to combine sva with survival analysis to validate genes in an independent dataset?
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2.9 years ago
a.e.c ▴ 30

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,

sva coxnet coxph survival RNA-seq • 599 views
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