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Table 1 Reproducibility of the microarray data

From: Reproducibility and reliability assays of the gene expression-measurements

  Uncorrected data After quantile correction
Experiment a Average number of genes with >50% inter-replicate variation r (P) b Slope c A.D d % Average number of genes with >50% inter-replicate variation r (P) b Slope c A.D d %
E-GEOD-53990: Arabidopsis data with 6 treatments and 3 replicates 8488/22810 (37%) 0.975 0.804 91% 2000/22810 (8.8%) 0.980 0.982 26%
E-GEOD-27822: Barley data with 2 treatments and 3 replicates 6433/22840 (28%) 0.992 1.22 34% 519/22840 (2.3%) 0.994 0.992 8.2%
E-GEOD-39950: Yeast data with 2 treatments and 3 replicates 1645/10928 (15%) 0.997 1.257 26% 396/10928 (3.6%) 0.997 0.980 12%
E-GEOD-49918: E. coli data with 4 treatments and 3 replicates 1059/10208 (10%) 0.996 1.032 28% 299/10208 (2.9%) 0.997 0.981 10%
E-GEOD-24524: E. coli data with 4 treatments and 2 replicates 837/10208 (8.2%) 0.995 0.999 22% 300/1028 (2.9%) 0.996 0.990 15%
  1. Different publicly available microarray data were analyzed using the Affymetrix Expression Console build 1.3.1.187 following the 3 Expression Arrays-RMA protocol. Both the corrected and uncorrected data were extracted. The Pearson correlations between the replicates were calculated on the log2 transformed data. Following our method, the average of the ratios’ deviations was also calculated in order to evaluate its usefulness compared to the correlation coefficient.
  2. aThe experiments are available at http://www.ebi.ac.uk/arrayexpress/experiments/browse.html, bThe average of Pearson correlations between the replicates in each experiment, cThe average of slopes of inter-replicate regression lines in each experiment, dThe average of the ratios’ deviations.