title: Spot intensity ratio statistics in two-channel microarray experiments.
abstract: In two-channel microarray experiments, the image analysis extracts red and green fluorescence intensities. The ratio of the two fluorescence intensities represents the relative abundance of the corresponding DNA sequence. The subsequent analysis is performed by taking a log-transformation of this ratio. Therefore, the statistical analyses depend on accuracy of the ratios calculated from the image analysis. However, not many studies have been proposed for developing more reliable ratio statistics. In this paper, we consider a new type of log-transformed ratio statistic. We compare the new ratio statistic with the conventional ratio statistic commonly used in two-channel microarray experiments. First, under the specific log-normal distributional assumption, we compare analytically the new statistics with the conventional ratio statistic. Second, we compare those ratio statistics using a two-channel microarray data obtained by hybridizing a mixture of mouse RNA and yeast in vitro transcript (IVT). Both comparisons show that the proposed ratio statistic performs better than the conventional one.
authors.affiliation: Department of Statistics, Seoul National University, Seoul, Korea. tspark@stats.snu.ac.kr
authors.forename: Taesung
authors.initials: T
authors.lastname: Park
authors.forename: Kiwoong
authors.initials: K
authors.lastname: Kim
authors.forename: Sung-Gon
authors.initials: SG
authors.lastname: Yi
authors.forename: Jin Hyuk
authors.initials: JH
authors.lastname: Kim
authors.forename: Yong-Sung
authors.initials: YS
authors.lastname: Lee
authors.forename: Seungyeoun
authors.initials: S
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D000818:Animals; D016477:Artifacts; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D005800:Genes, Fungal / Q000235:genetics; D007090:Image Interpretation, Computer-Assisted / Q000379:methods; D051379:Mice; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D012313:RNA / Q000032:analysis / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D012986:Software Validation