title: Application of the Taguchi method to the analysis of the deposition step in microarray production.
abstract: Every microarray experiment is affected by many possible sources of variability that may even corrupt biological evidence on analyzed sequences. We applied a "Taguchi method" strategy, based on the use of orthogonal arrays to optimize the deposition step of oligonucleotide sequences on glass slides. We chose three critical deposition parameters (humidity, surface, and buffer) at two levels each, in order to establish optimum settings. A L8 orthogonal array was used in order to monitor both the main effects and interactions on the deposition of a 25 mer oligonucleotide hybridized to its fluorescent-labeled complementary. Signal-background ratio and deposition homogeneity in terms of mean intensity and spot diameter were considered as significant outputs. An analysis of variance (ANOVA) was applied to raw data and to mean results for each slide and experimental run. Finally we calculated an overall evaluation coefficient to group together important outputs in one number. Environmental humidity and surface-buffer interaction were recognized as the most critical factors, for which a 50% humidity, associated to a chitosan-covered slide and a sodium phosphate + 25% dimethyl sulfoxide (DMSO) buffer gave best performances. Our results also suggested that Taguchi methods can be efficiently applied in optimization of microarray procedures.
authors.affiliation: Institute of Biomedical Technologies of the National Research Council, 20090 Milan, Italy. marco.severgnini@itb.cnr.it
authors.forename: Marco
authors.initials: M
authors.lastname: Severgnini
authors.forename: Linda
authors.initials: L
authors.lastname: Pattini
authors.forename: Clarissa
authors.initials: C
authors.lastname: Consolandi
authors.forename: Ermanno
authors.initials: E
authors.lastname: Rizzi
authors.forename: Cristina
authors.initials: C
authors.lastname: Battaglia
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.forename: Sergio
authors.initials: S
authors.lastname: Cerutti
mesh_terms: D000465:Algorithms; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*