Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips

Background: Affymetrix GeneChips are a popular platform for performing whole-genome experiments on the transcriptome. There are a range of different calibration steps, and users are presented with choices of different background subtractions, normalisations and expression measures. We wished to establish which of the calibration steps resulted in the biggest uncertainty in the sets of genes reported to be differentially expressed. Results: Our results indicate that the sets of genes identified as being most significantly differentially expressed, as estimated by the z-score of fold change, is relatively insensitive to the choice of background subtraction and normalisation. However, the contents of the gene list are most sensitive to the choice of expression measure. This is irrespective of whether the experiment uses a rat, mouse or human chip and whether the chip definition is made using probe mappings from Unigene, RefSeq, Entrez Gene or the original Affymetrix definitions. It is al...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Andrew P. Harrison, Caroline E. Johnston, Christine A. Orengo
• Keywords: Background Subtraction, BMCBI 2007, Calibration, Expression Measure