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Table 1 Estimates of array variance, var(earray), for three Illumina arrays types for normalized and raw data.

From: Estimates of array and pool-construction variance for planning efficient DNA-pooling genome wide association studies

  1M-Single 1M-Duo 660-Quad
Normalized data Var(e array ) (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(e array ) (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(e array ) (1) 12 45(2) 360
Number of arrays
(arrays/pool)
24 (2/pool) 32 (4/pool) 72 (6 or 12/pool)
  1. 1Each paired array comparison is treated as an independent estimate of array variance, the average of which is reported in this table.
  2. 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.