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Published online 3 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 4 e46
© 2004 Oxford University Press

Identification and handling of artifactual gene expression profiles emerging in microarray hybridization experiments

Leonid Brodsky*, Andrei Leontovich1, Michael Shtutman and Elena Feinstein

Quark Biotech Inc./QBI Enterprises Ltd, Weizmann Science Park, POB 4071, Ness Ziona 70400 Israel and 1 Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia

*To whom correspondence should be addressed. Tel: +972 8 9389188 ext. 119; Fax: +9728 9406476; Email: mbrodsky{at}actcom.co.il

Mathematical methods of analysis of microarray hybridizations deal with gene expression profiles as elementary units. However, some of these profiles do not reflect a biologically relevant transcriptional response, but rather stem from technical artifacts. Here, we describe two technically independent but rationally interconnected methods for identification of such artifactual profiles. Our diagnostics are based on detection of deviations from uniformity, which is assumed as the main underlying principle of microarray design. Method 1 is based on detection of non-uniformity of microarray distribution of printed genes that are clustered based on the similarity of their expression profiles. Method 2 is based on evaluation of the presence of gene-specific microarray spots within the slides’ areas characterized by an abnormal concentration of low/high differential expression values, which we define as ‘patterns of differentials’. Applying two novel algorithms, for nested clustering (method 1) and for pattern detection (method 2), we can make a dual estimation of the profile’s quality for almost every printed gene. Genes with artifactual profiles detected by method 1 may then be removed from further analysis. Suspicious differential expression values detected by method 2 may be either removed or weighted according to the probabilities of patterns that cover them, thus diminishing their input in any further data analysis.


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