title: Statistical validation of two sample comparison methods for oligonucleotide microarray in rat ischemia model.
abstract: In gene expression analyses using a high-density oligonucleotide array in a rat ischemia model, two comparison methods, "pair-wise comparison" and "sample average comparison", were evaluated based on statistical methods. The reliability of the elements screened with a 1.2 to 10-fold threshold was also evaluated. In pair-wise comparisons, most of the elements were significantly independent of the threshold value, with the percentage of significant elements remaining above 95%, when screened at 2.5-fold or higher threshold value. Pair-wise comparison structurally provided strict screening, which resulted in genes that were not selected despite significant alterations in expression. Screening by "sample average comparison" resulted in elements with low probability of significance, which suggested the necessity for increasing the reliability by additional statistical analyses after screening. When genes with altered expression were screened using an oligonucleotide array, marked differences in the numbers and reliability were proved to exist among elements screened by each sample comparison method.
authors.affiliation: Division of Genomic Epidemiology and Clinical Trials, Advanced Medical Research Center, Nihon University School of Medicine, Oyaguchi-Kami Machi, Tokyo 173-8610, Japan.
authors.forename: Megumi Sugahara
authors.initials: MS
authors.lastname: Kobayashi
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Toshihito
authors.initials: T
authors.lastname: Nagata
authors.forename: Yayoi
authors.initials: Y
authors.lastname: Nishida
authors.forename: Koichi
authors.initials: K
authors.lastname: Ishikawa
authors.forename: Satoshi
authors.initials: S
authors.lastname: Asai
mesh_terms: D000818:Animals; D002545:Brain Ischemia / Q000378:metabolism*; D004195:Disease Models, Animal; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D051381:Rats; D017208:Rats, Wistar