Fig. 2

Box plots showing the median, first quartile, third quartile, and range of CV (coefficient of variance) for all 952 HKG defined by nine different normalization algorithms (a) and for the subset of 42 HKG common to all nine normalization methods (b) . a The median values (range) of CV in 952 HKGs defined by RPKM and TC are 0.67 (0.65–0.69) and 0.44 (0.41–0.45), respectively; whereas the mean values of CV defined by UQ, Median, Quantile, TMM, DESeq, TPM and Library size are 0.31 (0.28–0.33), 0.29 (0.27–0.31), 0.29 (0.26–0.31), 0.31 (0.29–0.33), 0.30 (0.27–0.32), 0.29 (0.27–0.31), 0.29 (0.26–0.31), respectively. b The median values (range) of CV in 42 common HKGs defined by RPKM and TC are 0.67 (0.65–0.69) and 0.43 (0.42–0.45), respectively; whereas the mean values of CV defined by UQ, Median, Quantile, TMM, DESeq, TPM and Library size are 0.28 (0.26–0.31), 0.25 (0.23–0.28), 0.25 (0.22–0.29), 0.26 (0.24–0.30), 0.25 (0.22–0.29), 0.25 (0.23–0.28), 0.25 (0.22–0.28), respectively. TC: total counts; UQ: upper quartile; TMM: trimmed mean of M-values; TPM: transcripts per kilobase million; RPKM: reads per kilobase per million mapped reads; e (see Materials and Methods section for details)