On the causes of outliers in Affymetrix GeneChip data
- Upton, Graham JG
- Sanchez Graillet, Olivia
- Rowsell, Joanna
- Arteaga-Salas, Jose M
- Graham, Neil S
- Stalteri, Maria A
- Memon, Farhat N
- May, Sean T
- Harrison, Andrew P
DOIAbstract
Upton GJG, Sanchez Graillet O, Rowsell J, et al. On the causes of outliers in Affymetrix GeneChip data. Briefings in functional genomics and proteomics. 2009;8(3):199--212.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
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