VarMixt: efficient variance modelling for the differential analysis of replicated gene expression data.
BACKGROUND
Identifying differentially regulated genes in experiments comparing two experimental conditions is often a key step in the microarray data analysis process. Many different approaches and methodological developments have been put forward, yet the question remains open.


RESULTS
Varmixt is a powerful and efficient novel methodology for this task. It is based on a flexible and realistic variance modelling strategy. It compares favourably with other popular techniques (standard t-test, SAM and Cyber-T). The relevance of the approach is demonstrated with real-world and simulated datasets. The analysis strategy was successfully applied to both a 'two-colour' cDNA microarray and an Affymetrix Genechip. Strong control of false positive and false negative rates is proven in large simulation studies.


BACKGROUND
The R package is freely available at http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html


BACKGROUND
delmar@inapg.inra.fr


BACKGROUND
http://www.inapg.inra.fr/ens_rech/mathinfo/recherche/mathematique/outil.html.
Delmar
Paul
P
Laboratoire MAS Ecole Centrale Paris, Grande Voie des vignes, 92295 Chatenay Malabry, France. delmar@inapg.inra.fr
Robin
Stéphane
S
Daudin
Jean Jacques
JJ
D000465:Algorithms; D000704:Analysis of Variance; D003198:Computer Simulation; D004261:DNA Replication / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D014644:Genetic Variation / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software