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Online
Journal of Bioinformatics ©
Volume 7(1): 1-14, 2006.
A correction for expression value dependencies
in Affymetrix.
Broemel F1,
Kruse E2, Neuhäuser M3, Dürig J4, JÖckel
KH5
1Institute for Medical Informatics, Biometry and
Epidemiology, University Hospital, Essen D-45122, 2Department of
Botany, Faculty of Biology, Technical University Darmstadt, Darmstadt D-64287,
Institute for Medical Informatics, Biometry and Epidemiology, University Hospital,
Essen D-45122, 4Department of Hematology, University Hospital, Essen
D-45122, 5Institute for Medical Informatics, Biometry and
Epidemiology, University Hospital, Essen D-45122, Germany
ABSTRACT
Broemel F, Kruse E, Neuhäuser M, Dürig J, JÖckel KH A correction
for expression value dependencies in Affymetrix, Onl J Bioinform., 7 (1) : 1-14,
2006. Affymetrix oligonucleotide arrays measure the expression of
transcripts in biological samples. As with other high-density
oligonucleotide expression arrays, expression data generated by Affymetrix hides/influences significant biological
information. A correction for this influence using linear regression is
reported. The correction uses 3'/5'-ratios and a scaling factor to quantify the
effect. These corrections can be applied to other data sets produced by Affymetrix.
Keywords:
Microarray, Affymetrix, Technical Parameters.