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Removing intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells

Jianqing Fan Yongxiong Chen Hiu Man Chan Paul KH Tam Yi Ren

Data Analysis mathscidoc:1912.43353

Proceedings of the National Academy of Sciences, 102, (49), 17751-17756, 2005.12
A semilinear in-slide model is introduced to remove the intensity effect in the scanning process. It is demonstrated that the intensity effect can be estimated accurately and removed effectively. This normalization step is vital for Affymetrix arrays to reveal relevant biological results when comparing gene expression in multiple arrays. The normalized expression ratios are analyzed further by a modified two-sample <i>t</i> test along with a sieved permutation scheme for computing <i>P</i> values. The improved specificity and sensitivity are demonstrated by using a study on the impact of macrophage migration inhibitory factor (MIF) reduction in neuroblastoma cells. With semilinear in-slide model analysis, expression of 166 genes was altered with a <i>P</i> value no greater than 0.001. Among those genes, 44 were altered &gt;2-fold. MIF-regulated genes associated with tumor development including IL-8 and <i>C</i>-<i>met</i>, which are overexpressed
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@inproceedings{jianqing2005removing,
  title={Removing intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells},
  author={Jianqing Fan, Yongxiong Chen, Hiu Man Chan, Paul KH Tam, and Yi Ren},
  url={http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20191221113907776108913},
  booktitle={Proceedings of the National Academy of Sciences},
  volume={102},
  number={49},
  pages={17751-17756},
  year={2005},
}
Jianqing Fan, Yongxiong Chen, Hiu Man Chan, Paul KH Tam, and Yi Ren. Removing intensity effects and identifying significant genes for Affymetrix arrays in macrophage migration inhibitory factor-suppressed neuroblastoma cells. 2005. Vol. 102. In Proceedings of the National Academy of Sciences. pp.17751-17756. http://archive.ymsc.tsinghua.edu.cn/pacm_paperurl/20191221113907776108913.
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