I am new to RNA-seq analysis with bioconductor. I am wondering if I can use DESeq2 directly to perform survival analysis (e.g. Cox regression)? If not directly, do I understand correctly that we should do rlog or vst transformation on the count data before running Cox regression separately?
Second question is I have RNA-seq dataset with 1000 samples (20000 genes), it seems to be prohibitive to run rlog on this dataset with problem of running out of memory, any suggestion on ways to get around that?
Is there any other DE analysis packages (edgeR, limma, etc) that can perform survival analysis in addition to linear models?