I have RNAseq results from NovaSeq and after doing some differential gene expression with DESeq2, I will like to explore the Elastic Net model to select features that differentiate my two conditions.
However, I haven't been able to find a nice workflow or guidance about how to run this analysis. So, I have a couple of specific questions.
- Should I employ VST corrected gene expression as an input for the elastic net model
- Any suggestions about how many hyperparameters (lambda) to evaluate
- My dataset is small and this is exploratory, so I plan to do LOOCV (Leave-one-out cross-validation), any thoughts about it
- Anyone knows of a tutorial, repository or such with start to end Elastic Net for RNA-seq data