Analysis of a simulated microarray dataset: comparison of methods for data normalisation and detection of differential expression (open access publication).
Microarrays allow researchers to measure the expression of thousands of genes in a single experiment. Before statistical comparisons can be made, the data must be assessed for quality and normalisation procedures must be applied, of which many have been proposed. Methods of comparing the normalised data are also abundant, and no clear consensus has yet been reached. The purpose of this paper was to compare those methods used by the EADGENE network on a very noisy simulated data set. With the a priori knowledge of which genes are differentially expressed, it is possible to compare the success of each approach quantitatively. Use of an intensity-dependent normalisation procedure was common, as was correction for multiple testing. Most variety in performance resulted from differing approaches to data quality and the use of different statistical tests. Very few of the methods used any kind of background correction. A number of approaches achieved a success rate of 95% or above, with relatively small numbers of false positives and negatives. Applying stringent spot selection criteria and elimination of data did not improve the false positive rate and greatly increased the false negative rate. However, most approaches performed well, and it is encouraging that widely available techniques can achieve such good results on a very noisy data set.
Institute for Animal Health, Compton, UK (IAH_C). michael.watson@bbsrc.ac.uk
Michael
M
Watson
Mónica
M
Pérez-Alegre
Michael Denis
MD
Baron
Céline
C
Delmas
Peter
P
Dovc
Mylène
M
Duval
Jean-Louis
JL
Foulley
Juan José
JJ
Garrido-Pavón
Ina
I
Hulsegge
Florence
F
Jaffrézic
Angeles
A
Jiménez-Marín
Miha
M
Lavric
Kim-Anh
KA
Lê Cao
Guillemette
G
Marot
Daphné
D
Mouzaki
Marco H
MH
Pool
Christèle
C
Robert-Granié
Magali
M
San Cristobal
Gwenola
G
Tosser-Klopp
David
D
Waddington
Dirk-Jan
DJ
de Koning
D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D005060:Europe; D020869:Gene Expression Profiling / Q000706:statistics & numerical data*; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D012984:Software