Detecting spatial patterns in biological array experiments

被引:16
作者
Root, DE [1 ]
Kelley, BP [1 ]
Stockwell, BR [1 ]
机构
[1] Whitehead Inst Biomed Res, Cambridge, MA 02142 USA
关键词
assay development; error detection; quality assurance; quality control;
D O I
10.1177/1087057103254282
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Chemical genetic screening and DNA and protein microarrays are among a number of increasingly important and widely used biological research tools that involve large numbers of parallel experiments arranged in a spatial array. It is often difficult to ensure that uniform experimental conditions are present throughout the entire array, and as a result, one often observes systematic spatially correlated errors, especially when array experiments are performed using robots. Here, the authors apply techniques based on the discrete Fourier transform to identify and quantify spatially correlated errors superimposed on a spatially random back-round. They demonstrate that these techniques are effective in identifying common spatially systematic errors in high-throughput 384-well microplate assay data. In addition, the authors employ a statistical test to allow for automatic detection of such errors. Software tools for using this approach are provided.
引用
收藏
页码:393 / 398
页数:6
相关论文
共 6 条
[1]  
Gonzalez R.C., 1992, DIGITAL IMAGE PROCES
[2]   DNA microarrays and beyond: completing the journey from tissue to cell [J].
Mills, JC ;
Roth, KA ;
Cagan, RL ;
Gordon, JI .
NATURE CELL BIOLOGY, 2001, 3 (08) :E175-E178
[3]  
Oppenheim A. V., 1989, DISCRETE TIME SIGNAL
[4]  
Ripley B. D., 1981, SPATIAL STAT
[5]   Chemical genetics: Ligand-based discovery of gene function [J].
Stockwell, BR .
NATURE REVIEWS GENETICS, 2000, 1 (02) :116-125
[6]  
WINOGRAD S, 1978, MATH COMPUT, V32, P175, DOI 10.1090/S0025-5718-1978-0468306-4