Nucleic Acids Research, 2002, Vol. 30, No. 4 e15
© 2002 Oxford University Press
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
1Department of Statistics, 2Division of Biostatistics, 3Department of Molecular and Cell Biology, 4Functional Genomics Laboratory and 5Neurogenomics Center, Helen Wills Neuroscience Institute, University of California, Berkeley, CA 94720-3860, USA and 6Division of Genetics and Bioinformatics, The Walter and Eliza Hall Institute, Melbourne, Australia
There are many sources of systematic variation in cDNA microarray experiments which affect the measured gene expression levels (e.g. differences in labeling efficiency between the two fluorescent dyes). The term normalization refers to the process of removing such variation. A constant adjustment is often used to force the distribution of the intensity log ratios to have a median of zero for each slide. However, such global normalization approaches are not adequate in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. This article proposes normalization methods that are based on robust local regression and account for intensity and spatial dependence in dye biases for different types of cDNA microarray experiments. The selection of appropriate controls for normalization is discussed and a novel set of controls (microarray sample pool, MSP) is introduced to aid in intensity-dependent normalization. Lastly, to allow for comparisons of expression levels across slides, a robust method based on maximum likelihood estimation is proposed to adjust for scale differences among slides.
* To whom correspondence should be addressed at: Department of Statistics, University of California, 367 Evans Hall, #3860 Berkeley, CA 94720-3860, USA. Tel: +1 510 642 2781; Fax: +1 510 642 7892; Email: terry{at}stat.berkeley.eduThe authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors
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