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These and other continuous features were then normalized to the (0, 1) interval as described (e.g., see Supplementary Figure 5 in Garcia et al., 2011), except a trimmed normalization was implemented to prevent outlier values from distorting the normalized distributions.

This normalization was implemented in BASE using scripts developed by Ola Spjuth of Linnaeus Centre for Bioinformatics (http://www.lcb.uu.se/baseplugins.php).php

Normalization was implemented using the edgeR package in R [ 56].

In ArrayVision 8.0, Lowess normalization was implemented to remove dye effects.

Finally, an additive attention model, where attention does not contribute to normalization was implemented as: (8) (9) Note, that in Eqns  (6) and (8), β is still multiplied by c2, as it should not affect the second half of the numerator for conditions when the surround stimulus had 0% contrast.

Between-array normalization was implemented using the Aquantile method in the Limma package in R (http://www.R-project.org/) to ensure the A-values (average intensities) have the same empirical distribution across arrays leaving the M-values (log2-ratios) unchanged [ 42– 42].

Digital normalization is implemented in the script normalize-by-median.py.

Best-so-far search using min max normalization is implemented in the two methods.

The actual normalization methods, such as Robust Multi-array Average (RMA), Li-Wong (dChip), loess, quantile, robust spline and variance stabilizing normalization, are implemented as parameters of the tools [ 11, 12].

The structure factors can be normalized to obtain Equation (3): (3) or Equation (4): (4) both normalizations are implemented in TRAVIS.[ 27] Previously,[ 40] it was shown that 300 ion pairs are enough to reproduce all features above 0.24 Å−1.

Consequently, a normalization procedure was implemented in each modal matrix by dividing in each row by the higher numerical absolute value.