Statistical challenges in the analysis of two-dimensional difference gel electrophoresis experiments using DeCyder™

被引：50

作者：

Fodor, IK ^{[1
]}

Nelson, DO

Alegria-Hartman, M

Robbins, K

Langlois, RG

Turteltaub, KW

Corzett, TH

McCutchen-Maloney, SL

机构：

[1] Lawrence Livermore Natl Lab, Computat Directorate, Livermore, CA 94550 USA

[2] Lawrence Livermore Natl Lab, Biosci Directorate, Livermore, CA USA

来源：

BIOINFORMATICS | 2005年 / 21卷 / 19期

关键词：

D O I：

10.1093/bioinformatics/bti612

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Motivation: The DeCyder software (GE Healthcare) is the current state-of-the-art commercial product for the analysis of two-dimensional difference gel electrophoresis (2D DIGE) experiments. Analyses complementing DeCyder are suggested by incorporating recent advances from the microarray data analysis literature. A case study on the effect of smallpox vaccination is used to compare the results obtained from DeCyder with the results obtained by applying moderated t-tests adjusted for multiple comparisons to DeCyder output data that was additionally normalized. Results: Application of the more stringent statistical tests applied to the normalized 2D DIGE data decreased the number of potentially differentially expressed proteins from the number obtained from DeCyder and increased the confidence in detecting differential expression in human clinical studies.

引用

页码：3733 / 3740

页数：8

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