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Table 1 Design of spike-in experiment. The spike-in controls are two sets of ten synthesized RNA mixtures derived from the Adenovirus E1A transcriptome [31] with different concentrations in each set. The A mix was hybridized with Cy3 and the B Mix with Cy5 on each array, according to manufacturers recommendations, and in the recommended quantity.

From: Pre-processing Agilent microarray data

RNA spike-in name A Mix relative copy number B Mix relative copy number expected ratio A/B
(+)E1A_r60_1 10 10 1:1
(+)E1A_r60_n11 1.5 0.5 3:1
(+)E1A_r60_a20 100 100 1:1
(+)E1A_r60_3 3 9 1:3
(+)E1A_r60_a104 10 30 1:3
(+)E1A_r60_a107 30 10 3:1
(+)E1A_r60_a135 9 3 3:1
(+)E1A_r60_a22 10 100 1:10
(+)E1A_r60_a97 0.5 1.5 1:3
(+)E1A_r60_n9 100 10 10:1