Table 2 Estimates of array weights obtained from 1000 simulated microarray data sets. Means and standard deviations of the array weights estimated from 1000 simulated data sets assuming six different array variance scenarios are shown for normal and non-normal data using the full REML algorithm and the gene-by-gene update algorithm. Accurate estimates with small standard deviations are obtained using the full algorithm. The gene-by-gene update algorithm recovers weights which are generally only slightly flattened towards equal weights.

1

1.26

1.26 (0.04)

1.23 (0.07)

1.25 (0.04)

1.22 (0.07)

1.26

1.26 (0.04)

1.23 (0.07)

1.25 (0.04)

1.22 (0.07)

0.63

0.63 (0.01)

0.66 (0.03)

0.64 (0.01)

0.67 (0.03)

2

2.15

2.16 (0.15)

2.07 (0.14)

2.13 (0.13)

2.04 (0.14)

2.15

2.16 (0.14)

2.07 (0.13)

2.14 (0.14)

2.04 (0.14)

0.22

0.22 (0.00)

0.24 (0.01)

0.22 (0.00)

0.24 (0.01)

3

3.68

3.72 (0.33)

2.07 (0.14)

3.54 (0.29)

2.05 (0.15)

0.74

0.74 (0.04)

1.03 (0.06)

0.75 (0.04)

1.03 (0.06)

0.37

0.37 (0.02)

0.47 (0.02)

0.38 (0.01)

0.48 (0.02)

4

1.52

1.52 (0.03)

1.50 (0.05)

1.51 (0.03)

1.50 (0.05)

1.52

1.52 (0.03)

1.50 (0.04)

1.51 (0.03)

1.50 (0.05)

1.52

1.52 (0.03)

1.50 (0.05)

1.51 (0.03)

1.50 (0.05)

0.76

0.76 (0.01)

0.77 (0.02)

0.76 (0.01)

0.77 (0.02)

0.38

0.38 (0.01)

0.38 (0.01)

0.38 (0.01)

0.39 (0.01)

5

2.19

2.19 (0.05)

2.16 (0.07)

2.17 (0.05)

2.14 (0.07)

2.19

2.19 (0.05)

2.16 (0.07)

2.17 (0.05)

2.14 (0.07)

2.19

2.19 (0.05)

2.15 (0.07)

2.17 (0.05)

2.14 (0.07)

0.44

0.44 (0.01)

0.45 (0.01)

0.44 (0.01)

0.45 (0.01)

0.22

0.22 (0.00)

0.22 (0.00)

0.22 (0.00)

0.23 (0.00)

6

3.44

3.44 (0.12)

3.00 (0.13)

3.37 (0.12)

2.95 (0.13)

1.72

1.72 (0.04)

1.78 (0.06)

1.72 (0.04)

1.77 (0.06)

0.86

0.86 (0.02)

0.89 (0.02)

0.86 (0.02)

0.89 (0.02)

0.57

0.57 (0.01)

0.59 (0.01)

0.58 (0.01)

0.60 (0.01)

0.34

0.34 (0.01)

0.36 (0.01)

0.35 (0.01)

0.36 (0.01)