I have raw counts per exon matrix and want to normalize and do a VST or log2 transform without running any differential expression (for downstream usage separate to DE), so I just need the VST/log2 count matrix.
Is it sufficient to simply run
estimateSizeFactors on the DEXseq object and then run
vstfrom DESeq2 (or
log2 + 1) on the normalized counts before exporting to a csv? are there reasons that VST or log transformations might not be appropriate for exon counts?