Background: Interpretation of gene expression microarrays requires a mapping from probe set to gene. On many\r\nAffymetrix gene expression microarrays, a given gene may be detected by multiple probe sets, which may deliver\r\ninconsistent or even contradictory measurements. Therefore, obtaining an unambiguous expression estimate of a\r\npre-specified gene can be a nontrivial but essential task.\r\nResults: We developed scoring methods to assess each probe set for specificity, splice isoform coverage, and\r\nrobustness against transcript degradation. We used these scores to select a single representative probe set for each\r\ngene, thus creating a simple one-to-one mapping between gene and probe set. To test this method, we evaluated\r\nconcordance between protein measurements and gene expression values, and between sets of genes whose\r\nexpression is known to be correlated. For both test cases, we identified genes that were nominally detected by\r\nmultiple probe sets, and we found that the probe set chosen by our method showed stronger concordance.\r\nConclusions: This method provides a simple, unambiguous mapping to allow assessment of the expression levels\r\nof specific genes of interest.
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