Table 1.
A summary of 23 normalization methods developed for unbalanced transcriptome data.
| No. | Method | Full name or description | Platform (Original) | Reference selection | Normalization method | Software |
|---|---|---|---|---|---|---|
| 1 | GRSN (Pelz et al., 2008) | Global rank-invariant set normalization | Oligo array | Subset | Lowess | R |
| 2 | Xcorr (Chua et al., 2006) | Cross-correlation normalization | cDNA array, Oligo array | Subset | Non-linear regression | Matlab |
| 3 | NVSA (Ni et al., 2008) | Non-parametric variable selection and approximation | Oligo array | Subset | Non-linear regression | Matlab |
| 4 | KDWL (Hsieh et al., 2011) | Kernel density weighted loess normalization | Oligo array | Subset | Loess | SAS |
| 5 | KDQ (Hsieh et al., 2011) | Kernel density quantile normalization | Oligo array | Subset | Quantile | SAS |
| 6 | IRON (Welsh et al., 2013) | Iterative rank-order normalization | Oligo array | Subset | Loess | C |
| 7 | LVS (Calza et al., 2008) | Least-variant set normalization | Oligo array | Subset | Non-linear regression | R |
| 8 | LVSmiR (Suo et al., 2010) | Modified least-variant set normalization | Oligo miRNA array | Subset | Non-linear regression | R |
| 9 | Invariants normalization (Pradervand et al., 2009) | Invariants normalization | Oligo miRNA array | Subset | Non-linear regression | R |
| 10 | HMM-normalization (Landfors et al., 2011) | HMM assisted normalization | Microarray, RNA-seq | Subset | Further subset normalization | R |
| 11 | BSN (Aanes et al., 2014) | Biological scaling normalization | RNA-seq | Subset | R | |
| 12 | SVR (Fujita et al., 2006) | Support vector regression | cDNA, Oligo array | Subset | Non-linear regression | |
| 13 | ISN (Li and Hung Wong, 2001) | Invariant set normalization (in dChip) | Oligo array | Subset | – | R |
| 14 | Spike-in controls (Choe et al., 2005; Lovén et al., 2012) | Spike-in standards | Microarray, RNA-seq | Negative controls | – | – |
| 15 | wlowess (Oshlack et al., 2007) | Weighted lowess normalization | cDNA array, Oligo array | Negative controls | Loess | R |
| 16 | wcloess (Wu et al., 2013) | Weighted cyclic loess normalization | Oligo miRNA array | Negative controls | Loess | R |
| 17 | SQN (Wu and Aryee, 2010) | Subset quantile normalization | Oligo array | Negative controls | Quantile | R |
| 18 | loessM (Risso et al., 2009) | loessM | two-color miRNA array | Entire set (median) | Loess | R |
| 19 | GPA normalization (Xiong et al., 2008) | Generalized procrustes analysis | cDNA array | Entire set (median) | GPA | |
| 20 | Non-normalization (Klinglmueller et al., 2011; Wang et al., 2012) | Using data that are background adjusted but not normalized | Oligo miRNA array | Entire set | None | R |
| 21 | WPRMA (Kim et al., 2007) | RMA using within-pedigree pool | Oligo array | Entire set | Quantile | R |
| 22 | CrossNorm (Cheng et al., 2016a) | Cross normalization | Oligo array | Entire set | Quantile | R |
| 23 | ICN (Cheng et al., 2016b) | Informative cross normalization | Oligo array | Entire set | Quantile | R |