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Table 1 Summary of HKG Datasets Defined in This Study Using 9 Different Normalization Methods

From: Defining housekeeping genes suitable for RNA-seq analysis of the human allograft kidney biopsy tissue

Normalization methods Expression ratio* Bias** Variance**
0–0.01 (%) 0.01–0.05 (%) 0.05–0.20 (%) 0.20–0.40 (%) 0.40–0.60 (%) 0.60–0.80 (%) 0.80–1.0 (%)
TC 396 (41.60) 473 (49.68) 78 (8.19) 1 (0.11) 1 (0.11) 0 (0) 3 (0.32) 0.74 0.55
UQ 216 (22.69) 612 (64.29) 115 (12.08) 3 (0.32) 4 (0.42) 1 (0.11) 1 (0.11) 0.45 0.21
Median 157 (16.49) 643 (67.54) 142 (14.92) 7 (0.74) 2 (0.21) 0 (0) 1 (0.11) 0.45 0.22
Quantile 125 (13.13) 655 (68.80) 161 (16.91) 6 (0.63) 3 (0.32) 1 (0.11) 1 (0.11) 0.42 0.18
TMM 236 (24.79) 599 (62.92) 108 (11.34) 4 (0.42) 4 (0.42) 0 (0) 1 (0.11) 0.47 0.23
DESeq 231 (24.26) 610 (64.08) 104 (10.89) 4 (0.42) 2 (0.21) 0 (0) 1 (0.11) 0.43 0.19
TPM 157 (16.49) 643 (67.54) 142 (14.92) 7 (0.74) 2 (0.21) 0 (0) 1 (0.11) 0.45 0.22
RPKM 603 (63.34) 319 (33.51) 26 (2.73) 2 (0.21) 0 (0) 0 (0) 2 (0.21) 1.04 1.03
Lib_size 202 (21.22) 617 (64.81) 123 (12.92) 7 (0.74) 2 (0.21) 0 (0) 1 (0.11) 0.43 0.20
  1. Abbreviations: TC total counts, UQ upper quantile, TMM trimmed mean of M-values, DESeq a differential expression package implemented in R, TPM transcripts per kilobase million, RPKM reads per kilobase per million mapped reads, Lib_size library size
  2. *The expression ratio of each housekeeping gene was calculated by its mean normalized read divided by the maximum reads in its corresponding HKG set
  3. **The bias and variance of each normalization method was calculated by the formulae