Skip to main content

Table 1 Data consistency for the dataset of 2009 genes (before 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 18 10 11 11 10 9 8 9 42 11 13 11 8 6 8 7 10 23 9 9
Aff.T2 0.1229 Aff.T2 11 7 9 8 5 7 6 36 19 15 9 10 9 5 6 7 23 9 8
Aff.T3 0.1112 0.0893 Aff.T3 10 7 10 11 10 11 37 12 10 9 8 7 11 9 9 22 8 12
Ame.T1 0.1548 0.1425 0.1587 Ame.T1 72 78 31 31 28 24 5 9 84 49 42 32 23 22 21 73 29
Ame.T2 0.1656 0.1701 0.1771 0.7562 Ame.T2 78 35 34 33 22 5 8 84 40 34 36 19 22 18 63 31
Ame.T3 0.1536 0.1521 0.1705 0.7821 0.7743 Ame.T3 28 28 28 23 5 9 87 43 38 29 19 21 20 67 28
Agi.T1 0.1307 0.1364 0.1732 0.3176 0.3325 0.3213 Agi.T1 81 53 19 5 9 33 20 17 88 38 38 22 29 63
Agi.T2 0.1453 0.161 0.1674 0.3281 0.3499 0.3362 0.839 Agi.T2 51 19 6 8 32 21 18 86 36 38 23 30 61
Agi.T3 0.114 0.1358 0.1369 0.258 0.2867 0.2637 0.5895 0.6818 Agi.T3 17 4 4 31 21 16 60 31 29 17 28 45
Aff.B1 0.5515 0.5478 0.5551 0.2755 0.3102 0.288 0.2661 0.2866 0.234 Aff.B1 16 13 25 18 16 20 17 19 40 24 21
Aff.B2 0.048 0.0877 0.0422 0.0612 0.0603 0.0664 0.0595 0.0681 0.047 0.1045 Aff.B2 14 4 7 9 5 9 9 33 6 10
Aff.B3 0.0667 0.0852 0.076 0.1191 0.111 0.1255 0.1132 0.1224 0.0856 0.1377 0.061 Aff.B3 8 6 8 9 7 9 40 9 12
Ame.B1 0.1719 0.1684 0.1836 0.9171 0.9144 0.9245 0.3525 0.368 0.2932 0.3168 0.0682 0.129 Ame.B1 48 40 34 21 23 20 73 31
Ame.B2 0.1059 0.0963 0.0801 0.5138 0.5063 0.4695 0.1445 0.1557 0.1145 0.1694 0.0754 0.0956 0.5403 Ame.B2 49 21 30 27 20 62 27
Ame.B3 0.0871 0.0835 0.0677 0.4045 0.3361 0.4771 0.1301 0.1396 0.0864 0.1431 0.0734 0.116 0.4397 0.529 Ame.B3 16 30 34 20 58 28
Agi.B1 0.1451 0.1614 0.178 0.3364 0.3613 0.3429 0.8965 0.9314 0.8457 0.2932 0.0646 0.1189 0.3775 0.1539 0.131 Agi.B1 37 38 23 29 62
Agi.B2 0.0969 0.0883 0.0912 0.1982 0.176 0.1955 0.3946 0.4142 0.2584 0.1668 0.1263 0.103 0.2066 0.2835 0.3004 0.3926 Agi.B2 73 21 30 69
Agi.B3 0.1105 0.094 0.0984 0.1985 0.1846 0.1944 0.4178 0.4358 0.3152 0.1825 0.1251 0.1221 0.2095 0.2699 0.3055 0.4334 0.8483 Agi.B3 24 33 70
Aff 0.266 0.3221 0.2698 0.2417 0.2466 0.2555 0.2324 0.2542 0.1889 0.5176 0.5015 0.6006 0.2699 0.1957 0.1976 0.2508 0.2346 0.2555 Aff 24 27
Ame 0.1522 0.1452 0.1364 0.7625 0.7245 0.78 0.2579 0.2733 0.2008 0.2616 0.0893 0.1419 0.8224 0.8208 0.771 0.2716 0.3197 0.3181 0.2772 Ame 36
Agi 0.1477 0.145 0.1552 0.3087 0.3047 0.3087 0.7209 0.7515 0.5939 0.2708 0.1204 0.1418 0.3346 0.2721 0.2744 0.7693 0.8285 0.8607 0.3045 0.3674 Agi