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On the causes of outliers in Affymetrix GeneChip data

2009; Oxford University Press; Volume: 8; Issue: 3 Linguagem: Inglês

10.1093/bfgp/elp027

1477-4062

Graham Upton, Olivia Sanchez-Graillet, Joanna Rowsell, José M. Arteaga-Salas, Neil S. Graham, Maria A. Stalteri, Farhat Naureen Memon, Sean May, Andrew Harrison,

Genomics and Chromatin Dynamics

We describe various types of outliers seen in Affymetrix GeneChip data. We have been able to utilise the data in the Gene Expression Omnibus to screen GeneChips across a range of scales, from single probes, to spatially adjacent fractions of arrays, to whole arrays, to whole experiments. In this review we describe a number of causes for why some reported intensities might be misleading on GeneChips.