Journal Article

Detection and Normalization of Biases Present in Spotted cDNA Microarray Data: A Composite Method Addressing Dye, Intensity-Dependent, Spatially-Dependent, and Print-Order Biases

Shizuka Uchida, Yuichiro Nishida, Kenji Satou, Shigeru Muta, Kosuke Tashiro and Satoru Kuhara

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 12, issue 1, pages 1-7
Published in print January 2005 | ISSN: 1340-2838
Published online January 2005 | e-ISSN: 1756-1663 | DOI:

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Microarrays are often used to identify target genes that trigger specific diseases, to elucidate the mechanisms of drug effects, and to check SNPs. However, data from microarray experiments are well known to contain biases resulting from the experimental protocols. Therefore, in order to elucidate biological knowledge from the data, systematic biases arising from their protocols must be removed prior to any data analysis. To remove these biases, many normalization methods are used by researchers. However, not all biases are eliminated from the microarray data because not all types of errors from experimental protocols are known. In this paper, we report an effective way of removing various types of biases by treating each microarray dataset independently to detect biases present in the dataset. After the biases contained in each dataset were identified, a combination of normalization methods specifically made for each dataset was applied to remove biases one at a time.

Keywords: cDNA microarray; normalization; print-order bias

Journal Article.  0 words. 

Subjects: Genetics and Genomics

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