Neurochemical Research

, Volume 31, Issue 6, pp 735–740 | Cite as

Statistical Validation of Two Sample Comparison Methods for Oligonucleotide Microarray in Rat Ischemia Model

  • Megumi Sugahara Kobayashi
  • Yasuo Takahashi
  • Toshihito Nagata
  • Yayoi Nishida
  • Koichi Ishikawa
  • Satoshi Asai
Original Paper


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.


Microarray Gene expression Pair-wise comparison Threshold Statistics Ischemia 



This work was supported by a Nihon University Research Grant for Assistants and Young Researchers (2004) (no. 04–038), a Nihon University Joint Research Grant for 2005 (no. 05-016), and by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan to promote advanced scientific research.


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Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Megumi Sugahara Kobayashi
    • 1
    • 2
  • Yasuo Takahashi
    • 1
  • Toshihito Nagata
    • 1
  • Yayoi Nishida
    • 1
  • Koichi Ishikawa
    • 2
  • Satoshi Asai
    • 1
  1. 1.Division of Genomic Epidemiology and Clinical Trials, Advanced Medical Research CenterNihon University School of MedicineTokyoJapan
  2. 2.Department of PharmacologyNihon University School of MedicineTokyoJapan

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