Hi,
I am trying to use glmnet to perform Cox analysis. I have 150 samples and for 30k genes I have gene counts.
These are the two questions I have.
How would I go about normalizing the gene counts to fit into the assumptions of
glmnet?How should I go about selecting a smaller subset of genes?
For point 1, I am thinking I can use vst (from DESeq2) or maybe voom (limma) with calcNormFactors (edgeR) but I am stuck wondering about the standardize = TRUE option from glmnet.
For point 2, I was using rowVars from DESeq2 after I had normalized my data with either vst or voom with calcNormFactors.
And so currently, I am stuck deciding what to do for points 1 and 2. Any help would be appreciated.
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