glmnet and RNA-seq data
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Entering edit mode
23 months ago
Anastaziel • 0

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.

1. How would I go about normalizing the gene counts to fit into the assumptions of glmnet?

2. 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.

glmnet cox RNA-Seq R DESeq2 • 889 views
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Entering edit mode

Hi, can you please checkout these two bioconductor forum posts to see if they answer your question? Both answers are from experts in the field and both are authors of edgeR/DEseq2: https://support.bioconductor.org/p/93732/ https://support.bioconductor.org/p/93160/

I think combined they will help you figure out the right way forward.