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Affymetrix GeneChip® Eukaryotic Poly-A RNA Control Kit
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How do I evaluate the sensitivity and efficiency of the labeling reaction based on the Poly-A Controls?
First, examine the Present call rate of the 3' probe set of the poly-A RNA control transcripts. Following the recommended dilutions, all four poly-A RNA controls should be routinely called as Present in a Standard Assay. The poly-A RNA control present at the lowest concentration, lys, is expected to be called as Present >70-percent of the time for the Small Sample Target Labeling Assay vII, and the other three controls should be routinely called as Present.

Next, the relative Signal intensities of the four transcripts should also be checked such that they follow the same order of increasing poly-A RNA control concentration as expected. Example data can be found in the Kit's package insert.