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Table 2 Comparative table of normalization methods

From: Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

  3-parameter lognormal method [this work] LOWESS [2.3] house-keeping genes globalization [7] A N O V A [9] variance stabilization [5, 6]
assumed stable character statistical data distribution constant ratio tendency expression levels of particular genes sum of signal data smallest differences in log(data) smallest differences in arsinh(data)
Can the assumption be verified? yes [22, 26] Figs. 1,2 no yes1 no no no
units for expression level z-score ratios to a reference ratios to the stable genes fraction (ppm) ratios to a reference statistical differences to a reference
data transformation for the adjustment subtraction of a constant non-linear no no linear on logarithms linear
numbers of data sets normalized in a calculation 1 2 1 1 all the sets to be compared 2
Can it compare multiple data sets without reference RNA? yes no yes yes yes no
amount of calculation medium medium least least vast large-medium
reproducibility yes Figs. 3,8 no Fig. 7 nt3 no [7] no2 no Fig. 6cd
Is the ratio tendency independent of signal intensity? yes Figs. 5,8 yes Fig. 6b nt3 no Fig. 6a no2 yes Fig. 6cd
Is the ratio variance independent of signal intensity? yes Figs. 5,8 no Fig. 6b[7] nt3 no Fig. 6a no2 yes Fig. 6cd
Can it find the level of additive noise in the data? yes no no no no no
  1. 1A possible method is as follows: three or more gene candidates are chosen for the stable expression. Among the candidates, the ratio of every pair of data for a microarray experiment are calculated. If the expression levels are stable, the ratios are also stable. Such a combination of genes, however, has not been reported. 2Data are not presented. 3Since the stable genes could not be found among the data sets used in this article, this method was not tested (also see a review article [11]).