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Table 3 Comparison of RDAM and SAM in the case of two, three or five replicates and 500 increased genes

From: Rank Difference Analysis of Microarrays (RDAM), a novel approach to statistical analysis of microarray expression profiling data

   FDR50 FDR True Positive False Positive
R p var RDAM SAM RDAM SAM RDAM SAM RDAM SAM
2R 0.3 55% 63% 33% - 4 - 2 -
  0.1 25% 49% 21% - 172 - 45 -
  0.05 9% 39% 11% 14% 281 23 35 4
  0.01 1% 26% 15% 23% 452 175 77 51
3R 0.3 42% 47% 17% - 55 - 11 -
  0.1 7% 28% 16% 20% 344 156 64 40
  0.05 3% 19% 13% 18% 409 246 60 54
  0.01 0% 11% 14% 22% 473 381 80 109
5R 0.3 17% 21% 18% 25% 261 264 58 88
  0.1 2% 4% 15% 20% 455 395 81 101
  0.05 0% 2% 16% 20% 472 419 87 106
  0.01 0% 0% 19% 19% 474 443 111 105
  1. Comparisons were made between two groups of two replicates. The first group is composed of synthetic data sets made from the experimental replicates Wt-t0a and Wt-t0b, in which 1000 genes (500 increased and 500 decreased) are changed, and the second group is composed of synthetic data sets without extra variation. Results are shown for increased genes. The first column (R), indicates the number of replicates used. The second column (p var), gives the p-value of the extra variation introduced to the changed genes. The third column displays the FDR50, and the fourth column (FDR) the real FDR corresponding to the set of genes selected at FDR = 20%. For the same level of selection, columns 5 and 6 give, respectively, the number of true and false positives.