DEGseq can analyze normalized transcript expression data, such as RPKM. To determine if RPGM value is also an appropriate input for DEGseq, we compared the values. Both RPGM and RPKM values, fold changes, and Z-scores were significantly correlated (their p-values: < 2.2e-16) (Figure S3A, B, C in Supplement 1). RPGM and RPKM showed similar MA plot distributions (Figure S3D, E in Supplement 1) and identified a similar ratio of significantly changed genes in alcoholic brains. The top 100 significantly changed transcripts were also mostly conserved (Figure S3F in Supplement 1). This indicates the validity of using our RPGM calculations in DEGseq analysis.
