Fig. 5

Estimated Normalization Factors Provide Strict Cutoffs for DESeq2 A Differential expression analysis by DESeq2 (adj. p-val < 0.01) using size factors estimated from DESeq2 (red) and the VSI model (purple) on \(3^\prime\) invariant regions. Note that DESeq2 calls normalization factors “size factors”. The more conservative VSI identified set (purple) is a strict subset of the DESeq2 identified significant set. B Consistency of differential expression calls across a broad range of plausible normalization factors. Genes are colored based on the reproducibility of statistically significant differential expression (DESeq2, adj. p val \(< 0.01\)) across 1000 iterations where normalization factors were sampled from the posterior distribution estimated by VSI. Points that appear as significant most often are also those that are called as significant using both DESeq2 size factors and VSI 3\(^\prime\) normalization (Panel A, purple)