title: Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases.
abstract: 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.
authors.affiliation: School of Material Science, Japan Advanced Institute of Science and Technology-1 Asahidai, Tatsunokuchi, Ishikawa 923-1292, Japan.
authors.forename: Shizuka
authors.initials: S
authors.lastname: Uchida
authors.forename: Yuichiro
authors.initials: Y
authors.lastname: Nishida
authors.forename: Kenji
authors.initials: K
authors.lastname: Satou
authors.forename: Shigeru
authors.initials: S
authors.lastname: Muta
authors.forename: Kosuke
authors.initials: K
authors.lastname: Tashiro
authors.forename: Satoru
authors.initials: S
authors.lastname: Kuhara
mesh_terms: D000465:Algorithms; D015982:Bias; D004396:Coloring Agents; D019295:Computational Biology; D016014:Linear Models; D016011:Normal Distribution; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000706:statistics & numerical data*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D004396:Coloring Agents