【論】Workman,2002,A new non-linear normalization ～

Christopher Workman, Lars Juhl Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik Bjørn Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak and Steen Knudsen
A new non-linear normalization method for reducing variability in DNA microarray experiments
Genome Biology 2002, 3:research0048.1-0048.16
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・マイクロアレイデータの新しい正規化の方法を提案する。
・実験対象のマイクロアレイをcDNAかGeneChipのどちらかに限定する場合が多いが、この論文では『両方に使えます』というのがウリ。
・データ
1.HIV-infected T-cells, 6サンプル, GeneChip
2.B.subtilis, 6サンプル, cDNA
・正規化法
1.Lowess(robust local-linear regression)
2.Invariant set
3.Qspline：提案法, R+Bioconductorに実装
4.Spatial
ほか

・結果「The applications of these methods to oligonucleotide arrays reduced the relative error between replicates by 5-10% compared with a standard global normalization method. Application to cDNA arrays showed improvements over the standard method and over Cy3-Cy5 normalization based on dye-swap replication.」
・問題点「Much of the literature addressing microarray normalization concerns cDNA array data, whereas only a few examples can be found for oligonucleotide arrays.」
・概要「Here we review microarray normalization techniques, present the qspline method and show its application to Affymetrix oligonucleotide arrays of human T-cell cultures and cDNA arrays of Bacillus subtilis and Arabidopsis thaliana.」
・目的「The goal of signal-dependent normalization is to make signal distributions comparable across the intensity range.」