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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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>We present updated best-route methods for Affymetrix GeneChip analysis and demonstrate that the degree of \"imbalance\" in gene expression has a significant effect on the performance of these methods.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-11-285","type":"journal-article","created":{"date-parts":[[2010,5,27]],"date-time":"2010-05-27T18:15:34Z","timestamp":1274984134000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Preferred analysis methods for Affymetrix GeneChips. II. 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