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Model selection and efficiency testing for normalization of cDNA microarray data.
Institute for Theoretical Biology, Humboldt-Universität, Invalidenstrasse 43, 10115 Berlin, Germany. m.futschik@biologie.hu-berlin.de
In this study we present two novel normalization schemes for cDNA microarrays. They are based on iterative local regression and optimization of model parameters by generalized cross-validation. Permutation tests assessing the efficiency of normalization demonstrated that the proposed schemes have an improved ability to remove systematic errors and to reduce variability in microarray data. The analysis also reveals that without parameter optimization local regression is frequently insufficient to remove systematic errors in microarray data.
PMID: 15287982 [PubMed - indexed for MEDLINE]
PMCID: PMC507885
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Cited by 6 PubMed Central articles
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A comparison on effects of normalisations in the detection of differentially expressed genes.
Chiogna M, Massa MS, Risso D, Romualdi C.
BMC Bioinformatics. 2009 Feb 13; 10:61. Epub 2009 Feb 13.
[BMC Bioinformatics. 2009]
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Profiling sex-biased gene expression during parthenogenetic reproduction in Daphnia pulex.
Eads BD, Colbourne JK, Bohuski E, Andrews J.
BMC Genomics. 2007 Dec 18; 8:464. Epub 2007 Dec 18.
[BMC Genomics. 2007]
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New insights about host response to smallpox using microarray data.
Esteves GH, Simoes AC, Souza E, Dias RA, Ospina R, Venancio TM.
BMC Syst Biol. 2007 Aug 24; 1:38. Epub 2007 Aug 24.
[BMC Syst Biol. 2007]
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