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Table 2 Data consistency for the dataset of 537 genes (after data filtering). The pair-wise log ratio correlation squared (LRr2, lower triangle) and the percentage of overlapping genes (POG, upper triangle) are listed. T1, T2, and T3 are technical replicates; B1, B2, and B3 are biological replicates. The last three rows/columns (Affymetrix (Aff), Amersham (Ame), and Agilent (Agi)) represent results from the average of the three biological replicates. Gene selection was based on fold-change ranking, and a total of 100 genes (50 genes from each regulation direction) were selected for each comparison. Black bold numbers represent intra-platform technical or biological consistency, or cross-platform concordance.

From: Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

  Aff.T1 Aff.T2 Aff.T3 Ame.T1 Ame.T2 Ame.T3 Agi.T1 Agi.T2 Agi.T3 Aff.B1 Aff.B2 Aff.B3 Ame.B1 Ame.B2 Ame.B3 Agi.B1 Agi.B2 Agi.B3 Aff Ame Agi
Aff.T1 Aff.T1 53 56 52 49 52 50 53 54 71 46 41 53 42 46 52 45 44 58 52 52
Aff.T2 0.5745 Aff.T2 44 51 53 51 48 47 46 70 46 45 53 41 41 47 43 43 61 48 47
Aff.T3 0.5902 0.4525 Aff.T3 52 51 52 53 54 53 69 37 37 53 36 39 53 38 37 48 46 47
Ame.T1 0.5341 0.53 0.572 Ame.T1 88 90 58 60 54 60 39 38 95 55 52 60 37 38 53 76 50
Ame.T2 0.5439 0.537 0.5836 0.9347 Ame.T2 89 56 58 52 59 40 39 92 57 51 58 36 36 55 77 48
Ame.T3 0.5486 0.5499 0.5768 0.9374 0.9482 Ame.T3 57 59 53 59 40 40 94 55 54 58 36 37 55 78 48
Agi.T1 0.4382 0.446 0.5163 0.564 0.5705 0.572 Agi.T1 89 78 57 33 40 59 35 37 89 44 50 50 49 69
Agi.T2 0.4676 0.4847 0.5405 0.5954 0.6009 0.6052 0.9613 Agi.T2 84 57 38 42 62 39 39 93 49 55 53 50 75
Agi.T3 0.4553 0.4617 0.5177 0.5687 0.5729 0.5796 0.9041 0.9419 Agi.T3 56 38 40 55 36 38 88 47 52 50 46 74
Aff.B1 0.858 0.8009 0.8076 0.664 0.6755 0.68 0.5682 0.6059 0.5822 Aff.B1 41 44 60 44 47 57 45 47 64 55 55
Aff.B2 0.4191 0.4626 0.361 0.3498 0.3524 0.3606 0.3054 0.334 0.3301 0.5029 Aff.B2 41 41 47 53 36 54 52 58 46 47
Aff.B3 0.3238 0.417 0.2726 0.3576 0.3766 0.3844 0.3515 0.3834 0.3774 0.4083 0.4451 Aff.B3 40 38 43 41 44 47 74 46 48
Ame.B1 0.5534 0.5502 0.5894 0.9767 0.9807 0.9818 0.5806 0.6129 0.5856 0.6871 0.3616 0.3806 Ame.B1 56 53 61 37 38 55 78 50
Ame.B2 0.4268 0.3686 0.3707 0.6163 0.6253 0.6093 0.313 0.3422 0.3289 0.4719 0.4917 0.2973 0.6297 Ame.B2 71 37 48 46 48 72 43
Ame.B3 0.4137 0.371 0.3575 0.579 0.5647 0.6168 0.3084 0.3389 0.3244 0.4624 0.5056 0.3427 0.5989 0.7859 Ame.B3 37 55 53 52 70 50
Agi.B1 0.4634 0.4739 0.5363 0.5885 0.594 0.5982 0.977 0.9889 0.9686 0.5979 0.3298 0.3784 0.6059 0.3348 0.3306 Agi.B1 47 52 51 50 74
Agi.B2 0.3926 0.3393 0.3296 0.3591 0.3581 0.3627 0.4694 0.5186 0.5031 0.4293 0.5678 0.3239 0.3674 0.5783 0.5682 0.5072 Agi.B2 85 53 45 72
Agi.B3 0.3888 0.3461 0.332 0.355 0.359 0.3598 0.4975 0.541 0.5335 0.4318 0.5659 0.353 0.3654 0.5435 0.5677 0.5349 0.9525 Agi.B3 53 46 78
Aff 0.6397 0.694 0.5684 0.5686 0.5842 0.5934 0.5141 0.5563 0.5432 0.7705 0.7688 0.7978 0.5942 0.5167 0.5437 0.5491 0.5396 0.5566 Aff 58 58
Ame 0.5379 0.4995 0.5108 0.842 0.8412 0.856 0.4661 0.5019 0.4805 0.6277 0.5041 0.3921 0.8639 0.8909 0.8765 0.4931 0.5547 0.5425 0.6341 Ame 51
Agi 0.4877 0.4581 0.4759 0.5176 0.5212 0.5249 0.7747 0.816 0.7989 0.5766 0.5354 0.4123 0.532 0.5341 0.5366 0.8137 0.8863 0.9037 0.6372 0.6098 Agi