Normalization for Affymetrix GeneChips.
OBJECTIVE
The high density oligonucleotide microarrays from Affymetrix (Affymetrix GeneChips) are very popular in biomedical research. They enable to study the expression of thousands of genes simultaneously. In experiments with multiple arrays, normalization techniques are used to reduce the so-called obscuring variation, i.e. the technical variation that is of non-biological origin. Several different normalization methods have been proposed during the last years.


METHODS
We review published results about the comparison of normalization methods proposed for Affymetrix GeneChips.


RESULTS
The quantile normalization seems to perform favorably regarding precision (low variance), accuracy (low bias), and practicability (low computing time). However, according to very recent results, this normalization method can have an impact on the biological variability and, therefore, appears to be less than optimal from this point of view.


CONCLUSIONS
Although the quantile normalization may be recommendable, more investigations based on more data sets are needed so that the different normalization methods can be evaluated on widely differing data.
Boes
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T
Institut für Medizinische Informatik, Biometrie und Epidemiologie, Universitätsklinikum Essen, Hufelandstr. 55, 45122 Essen, Germany. tanja.boes@medizin.uni-essen.de
Neuhäuser
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M
D000465:Algorithms; D003198:Computer Simulation; D015342:DNA Probes; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D008432:Mathematical Computing; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D012016:Reference Values; D017422:Sequence Analysis, DNA / Q000379:methods*
D015342:DNA Probes