Open AccessArraySolver: an algorithm for colour‐coded graphical display and Wilcoxon signed‐rank statistics for comparing microarray gene expression data
Author(s) -
Khan Haseeb Ahmad
Publication year - 2004
Publication title -
comparative and functional genomics
Language(s) - English
Resource type - Journals
eISSN - 1532-6268
pISSN - 1531-6912
DOI - 10.1002/cfg.369
Subject(s) - wilcoxon signed rank test , rank (graph theory) , computer science , data mining , microarray analysis techniques , gene chip analysis , microarray databases , statistical hypothesis testing , software , microarray , statistics , mann–whitney u test , mathematics , gene , gene expression , biology , genetics , combinatorics , programming language
The massive surge in the production of microarray data poses a great challenge for proper analysis and interpretation. In recent years numerous computational tools have been developed to extract meaningful interpretation of microarray gene expression data. However, a convenient tool for two‐groups comparison of microarray data is still lacking and users have to rely on commercial statistical packages that might be costly and require special skills, in addition to extra time and effort for transferring data from one platform to other. Various statistical methods, including the t ‐test, analysis of variance, Pearson test and Mann–Whitney U test, have been reported for comparing microarray data, whereas the utilization of the Wilcoxon signed‐rank test, which is an appropriate test for two‐groups comparison of gene expression data, has largely been neglected in microarray studies. The aim of this investigation was to build an integrated tool, ArraySolver, for colour‐coded graphical display and comparison of gene expression data using the Wilcoxon signed‐rank test. The results of software validation showed similar outputs with ArraySolver and SPSS for large datasets. Whereas the former program appeared to be more accurate for 25 or fewer pairs ( n ≤ 25), suggesting its potential application in analysing molecular signatures that usually contain small numbers of genes. The main advantages of ArraySolver are easy data selection, convenient report format, accurate statistics and the familiar Excel platform. Copyright © 2004 John Wiley & Sons, Ltd.