Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

We present a new wholly defined Affymetrix spike-in dataset consisting of 18 microarrays. Over 5700 RNAs are spiked in at relative concentrations ranging from 1- to 4-fold, and the arrays from each condition are balanced with respect to both total RNA amount and degree of positive- versus negative-fold change. We use this new Platinum Spike dataset to evaluate microarray analysis routes and contrast the results to those achieved using our earlier Golden Spike dataset.

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Zhu Q, Miecznikowski JC, Halfon MS