Table 1

Estimates of array variance, var(earray), for three Illumina arrays types for normalized and raw data.

1M-Single

1M-Duo

660-Quad


Normalized data Var(earray) (Range)

3.8 × 10-4

(2.2 × 10-4 - 6.6 × 10-4)

3.2 × 10-4

(1.6 × 10-4 - 6.3 × 10-4)

3.3 × 10-4

(2.5 × 10-4 - 4.9 × 10-4)


Raw data Var(earray) (Range)

2.9 × 10-3

(3.0 × 10-4 - 9.2 × 10-3)

9.0 × 10-4

(1.7 × 10-4 - 4.3 × 10-3)

2.7 × 10-3

(2.0 × 10-3 - 3.0 × 10-3)


Number of pools

12

8

7


Number of comparisons, var(earray)(1)

12

45(2)

360


Number of arrays

(arrays/pool)

24 (2/pool)

32 (4/pool)

72 (6 or 12/pool)


1Each paired array comparison is treated as an independent estimate of array variance, the average of which is reported in this table.

2One array, in all 3 comparisons in which it was involved, produced extreme outlier var(earray) values and was removed from all analysis; hence, there are 45 instead of 48 var(earray) for the 1M-Duo arrays.

Earp et al. BMC Medical Genomics 2011 4:81   doi:10.1186/1755-8794-4-81

Open Data