|
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
|
- 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
- *The expression ratio of each housekeeping gene was calculated by its mean normalized read divided by the maximum reads in its corresponding HKG set
- **The bias and variance of each normalization method was calculated by the formulae
