Quality control of microarray analysis. (A) RNA quality controls made with the 2100 expert software and the 2100 bioanalyzer. The first spike, corresponding to the nanomarker, is an internal control. The second spike corresponds to the 18S RNA and the third spike to the 28S RNA. A good-quality profile is defined by 4 indicators: the basal line must be regular, the 28S spike must be higher than the 18S spike, the 28S/18S ratio must be between 1.5 and 2.5, and the integrity number must be between 1 and 10. The 28S/18S ratio and the integrity number were 1.9 and 10, respectively, for populations 2N (a), 4N (b) and 16N (d), and 2.0 and 10, respectively, for population 8N (c). (B) Example of analysis of the homogeneity level in terms of LogRatio (log of red and green intensities) on the surface of a 44K human whole genome array. Box X2 and Box Y1 correspond to box plot representation (R software) along all vertical (box X) and horizontal (box Y) lines of probes (200 × 400 interleaved). Results show that the mean value of LogRatio is around 0 (due to normalization) without fluctuations of more than 0.04. (C) Representative example of intensities of 2N, 4N, 8N, and 16N populations (Intensity 2) versus the pool (Intensity 1) for combined dye-swap experiments in Resolver software. Probes in red (up-regulated) or green (down-regulated) are calculated at P < .001. Blue probes (unchanged) are considered nondiscriminating between different population samples and the pool. Red lines correspond to levels of fold-change of ± 2. 2N: 887 gene signatures with 561 down-regulated and 326 up-regulated. 4N: 261 gene signatures with 109 down-regulated and 152 up-regulated. 8N: 232 gene signatures with 106 down-regulated and 126 up-regulated. 16N: 362 gene signatures with 241 down-regulated and 121 up-regulated.