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Table 1 Comparison of results from the simulated data. Comparison of numbers of genes in common declared significant (i.e., significantly differentially expressed) by simulated labs 1 through 6, the SLR-based fixed effexts and random effects meta-analyses, and the previously proposed P-value-based meta-analysis [2]. The (i, j)thelement of this table is the number of genes declared significant by both lab i and lab j, with F here representing the fixed effects meta-analysis, R the random effects meta-analysis, and T the "truth" behind the simulation model. P represents the meta-analysis based on P-values [2]. Each lab (and meta-analysis) had the False Discovery Rate (FDR) controlled at 0.05.

From: Combining Affymetrix microarray results

  Simulated Lab Meta-Analysis  
  1 2 3 4 5 6 Fixed Random P-value Truth
1 46 33 34 34 31 31 43 35 33 35
2   49 34 37 31 34 47 39 35 38
3    54 34 32 36 44 41 38 41
4     51 30 35 48 38 35 39
5      44 32 39 37 34 37
6       58 48 40 37 41
F        137 72 45 58
R         72 45 56
P          45 45
T           70