title: Normalization methods for analysis of microarray gene-expression data.
abstract: This paper investigates subset normalization to adjust for location biases (e.g., splotches) combined with global normalization for intensity biases (e.g., saturation). A data set from a toxicogenomic experiment using the same control and the same treated sample hybridized to six different microarrays is used to contrast the different normalization methods. Simple t-tests were used to compare two samples for dye effects and for treatment effects. The numbers of genes that reproducibly showed significant p-values for the unnormalized data and normalized data from different methods were evaluated for assessment of different normalization methods. The one-sample t-statistic of the ratio of red to green samples was used to test for dye effects using only control data. For treatment effects, in addition to the one-sample t-test of the ratio of the treated to control samples, the two-sample t-test for testing the difference between treated and control samples was also used to compare the two approaches. The method that combines a subset approach (median or lowess fit) for location adjustment with a global lowess fit for intensity adjustment appears to perform well.
authors.affiliation: Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA.
authors.forename: Yi-Ju
authors.initials: YJ
authors.lastname: Chen
authors.forename: Ralph
authors.initials: R
authors.lastname: Kodell
authors.forename: Frank
authors.initials: F
authors.lastname: Sistare
authors.forename: Karol L
authors.initials: KL
authors.lastname: Thompson
authors.forename: Suzanne
authors.initials: S
authors.lastname: Morris
authors.forename: James J
authors.initials: JJ
authors.lastname: Chen
mesh_terms: D015982:Bias; D003627:Data Interpretation, Statistical; D005456:Fluorescent Dyes; D020869:Gene Expression Profiling / Q000379:methods / Q000706:statistics & numerical data*; D015233:Models, Statistical; D016011:Normal Distribution; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000706:statistics & numerical data*
chemical_list: D005456:Fluorescent Dyes