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Table 3 Concordance between platforms using statistically significant expression ratios at p-value < 0.05 and at 1.5 and 2-fold threshold levels.1

From: Three microarray platforms: an analysis of their concordance in profiling gene expression

  No threshold 1.5-fold 2-fold
  GEM2 vs. Operon GEM2 vs. U133A Operon vs. U133A GEM2 vs. Operon GEM2 vs. U133A Operon vs. U133A GEM2 vs. Operon GEM2 vs. U133A Operon vs. U133A
Number of comparisons 2
Jurkat 1471 1678 1740 1096 1088 1220 588 614 749
L428 651 1394 750 580 1051 632 430 678 469
SUDHL 1400 1527 1707 1081 1177 1277 698 741 831
OCI-Ly3 1484 1834 1698 1285 1428 1333 814 900 903
LNCaP 1167 1170 2062 737 751 1252 369 404 696
MCF10A 1555 1429 1880 899 812 1118 405 409 559
Percent of concordance
Jurkat 97% 96% 98% 98% 99% 100% 99% 99% 100%
L428 96% 96% 98% 98% 98% 99% 99% 99% 100%
SUDHL 95% 97% 98% 97% 98% 99% 99% 99% 100%
OCI-Ly3 94% 96% 96% 95% 98% 98% 98% 99% 99%
LNCaP 93% 95% 96% 97% 98% 99% 99% 100% 100%
MCF10A 94% 95% 96% 98% 98% 99% 99% 99% 100%
Total number of comparisons
  7728 9032 9837 5678 6307 6832 3304 3746 4207
Total number of concordances
  7334 8650 9540 5509 6191 6755 3257 3719 4190
Percent agreement
  94.9% 95.8% 97.0% 97.0% 98.2% 98.9% 98.6% 99.3% 99.6%
Percent of data used 3
  54.0% 57.5% 60.4% 39.7% 40.2% 42.0% 23.1% 23.9% 25.8%
  1. 1GEM2: Incyte GEM2 arrays; Operon: Operon V2 arrays; U133A: Affymetrix Human Genome U 133A GeneChip arrays.
  2. 2Comparisons between two platforms were done only when the expressions of both platforms met the p-value and threshold criteria.
  3. 3Fraction of common expressions between two platforms to the total number of expressions found at p < 0.05 in both platforms.