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Table 1 Methods for transformation and normalization identified through literature search

From: Comparison of pre-processing methods for multiplex bead-based immunoassays

Transformation
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 -
Normalization
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]
  1. Methods used in this work are marked with at least one asterisk. Own developed methods are marked with two asterisks. We have chosen the methods with three asterisks to test their effects on the data