A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays.

This difference is statistically significant: when the genes are divided into 10 bins based on depth or intensity, all bins up to the 80th percentile of intensity (less than a fluorescence intensity of 5500 or fewer than 30 000 reads) show a highly significant difference between the amount of variation added by the microarray chip versus the sequencing lane (Supplementary Figure S4).

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