PQN and DQN: Algorithms for expression microarrays

被引：23

作者：

Liu, Wei-Min ^{[1
]}

Li, Rui ^{[1
]}

Sun, James Z. ^{[1
]}

Wang, Jing ^{[1
]}

Tsai, Julie ^{[1
]}

Wen, Wei ^{[1
]}

Kohlmann, Alexander ^{[1
]}

Williams, P. Mickey ^{[1
]}

机构：

[1] Roche Mol Syst Inc, Pleasanton, CA 94588 USA

来源：

JOURNAL OF THEORETICAL BIOLOGY | 2006年 / 243卷 / 02期

关键词：

gene expression; hybridization; microarray; normalization; robustness;

D O I：

10.1016/j.jtbi.2006.06.017

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

An ideal expression algorithm should be able to tell truly different expression levels with small false positive errors and be robust to assay changes. We propose two algorithms. PQN is the non-central trimmed mean of perfect match intensities with quantile normalization. DQN is the non-central trimmed mean of differences between perfect match and mismatch intensities with quantile normalization. The quantiles for normalization can be either empirical or theoretical. When array types and/or assay change in a study, the normalization to common quantiles at the probe set level is essential. We compared DQN, PQN, RMA, GCRMA, DCHIP, PLIER and MAS5 for the Affymetrix Latin square data and our data of two sets of experiments using the same bone marrow but different types of microarrays and different assay. We found the computation for AUC of ROC at affycomp.biostat.jhsph.edu can be improved. (c) 2006 Elsevier Ltd. All rights reserved.

引用

页码：273 / 278

页数：6

共 19 条

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