Table 1 Methods for transformation and normalization identified through literature search

Name

Abbr. in paper

Reference

 Hyperbolic area sine*

asinh

[37]

 Box-Cox*

boxcox

[11]

 Log2*

log2

[5, 38]

 Linlog

[12]

 No***

no

-

 Variance stabilizing*

vst

[5, 38]

 Weighted Box-Cox**

boxcoxweights

-

Name

Abbr. in paper

Reference

 Contrast

[10]

 Cyclic loess

[10]

 Global mean

[39]

 Global median*

global

[39]

 Housekeeping genes

[17]

 Improved quantile**

quanimpr

-

 Invariant set

[10]

 Locally weighted scatterplot smoothing*

loess

[5]

 Peng’s method

[13]

 Quantile*

quantile

[5, 10, 38]

 Qspline

[10, 40]

 Robust quantile

[10]

 Robust spline*

rsn

[5, 38]

 Scaling/constant

[10]

 Spiked controls

[17]

 T-quantiles

[13]

 Tukey’s biweight scaling

[13]

 Variance stabilizing*

vsn

[5, 40]

 Z-score*

zscore

[41]