Design and structure of the Platinum Spike experiment. (A) Design of the Platinum Spike experiment. PCR products were collected into 28 distinct pools, and three independent in vitro transcription and labeling reactions were performed for each pool. Labeled cRNAs from each individual pool were then added at specified amounts to samples A and B to achieve the desired fold change differences between samples. Note that this method ensures that the relative concentrations of cRNAs from the same pool are always identical. Each sample was hybridized to three arrays (see Methods). (B) Structure of the 18 Platinum Spike arrays showing the three ways of normalization (normalization groups) used in the analysis. The technical normalization group normalizes each set of technical replicates for a total of six normalizations. The conditional normalization group uses all of the arrays from the same condition, a total of two normalizations. The all normalization group consists of a single normalization using all of the arrays in the experiment.