A Nested Parallel Experiment Demonstrates Differences in Intensity-Dependence Between RNA-Seq and Microarrays

We carried out a parallel nested experiment performed simultaneously on RNA-Seq and microarrays that systematically split variation into four stages (treatment, biological variation, library preparation, and chip/lane noise), allowing a separation and comparison of the sources of variation in a well-controlled cellular system, Saccharomyces cerevisiae. Nested design. Two conditions (E for ethanol and G for glucose as sole carbon source), each grown on two biological replicates (1 and 2), prepared in two technical preparations (A and B), then hybridized to two chips (1 and 2) This submission represents microarray component of study.