VarMixt: Efficient variance modelling for the differential analysis of replicated gene expression data

Bioinformatics

Volumn 21, Issue 4, 2005, Pages 502-508

  Delmar, Paul ^a,c   Robin, Stéphane ^b   Daudin, Jean Jacques ^b  

^a Ecole Centrale de Paris   (France)

^b AgroParisTech   (France)

^c Laboratoires Fournier SA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; ANALYSIS OF VARIANCE; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE REPLICATION; INFORMATION PROCESSING; INTERNET; METHODOLOGY; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; SIMULATION; STATISTICAL MODEL; STUDENT T TEST;

EID: 14644429669     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti023     Document Type: Article

References (15)

1. Baldi,P. and Long,A. (2001) A bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics, 17, 509-519.
2. Cole,S.W., Galic,Z. and Zack,J.A. (2003) Controlling false-negative errors in microarray differential expression analysis: a prim approach. Bioinformatics, 19, 1808-1816.
3. Delmar,P., Robin,S., Tronik-Leroux,D. and Daudin,J. (2005) Mixture model on the variance for the differential analysis of gene expression data. J. R. Stat. Soc., Ser. C, 54, 31-50.
4. Draghici,S., Kulaeva,O., Hoff,B., Petrov,A., Shams,S. and Tainsky,M.A. (2003) Noise sampling method: an ANOVA approach allowing robust selection of differentially regulated genes measured by DNA microarrays. Bioinformatics, 19, 1348-1359.
5. Gentleman,R. and Carey,V. (2002) Bioconductor. R News, 2, 11-16.
6. Hughes,T., Marton,M., Jones,A., Roberts,C., Stoughton,R., Armour,C., Bennett,H., Coffey,E., Dai,H. and He,Y. (2000) Functional discovery via a compendium of expression profiles. Cell, 102, 109-126.
7. Irizarry,R.A., Bolstad,B.M., Collin,F., Cope,L.M., Hobbs,B. and Speed,T.P. (2003) Summaries of affymetrix genechip probe level data. Nucleic Acids Res., 31, e15.
8. Kerr,M., Afshari,C., Bennett,L., Bushel,P., Martinez,J., Walker,N. and Churchill,G. (2002) Statistical analysis of a gene expression microarray experiment with replication. Stat. Sinica, 12, 203-218.
9. Lönnstedt,I. and Speed,T. (2002) Replicated microarray data. Stat. Sinica, 12, 31-46.
10. Mary-Huard,T., Daudin,J.-J., Robin,S., Bitton,F., Cabannes,E. and Hilson, P. (2004) Spotting effect in microarray experiments. BMC Bioinformatics, 5, 63.
11. Rocke,D.M. and Durbin,B. (2003) Approximate variance-stabilizing transformations for gene-expression microarray data. Bioinformatics, 19, 966-972.
12. Schuchhardt,J., Beule,D., Malik,A., Wolski,E., Eickhoff,H., Lehrach,H. and Herzel,H. (2000) Normalization strategies for cdna microarrays. Nucleic Acids Res., 28, e41.
13. Tusher,V., Tibshirani,R. and Chu,G. (2001) Significance analysis of microarrays applied to ionizing radiation response. Proc. Nat Acad. Sci. USA, 98, 5116-5121.
14. Wang,S. and Ethier,S. (2004) A generalized likelihood ratio test to identify differentially expressed genes from microarray data. Bioinformatics, 20, 100-104.
15. Wolfinger,R.D., Gibson,G., Wolfinger,E.D., Bennett,L., Hamadeh,H., Bushel,P., Afshari,C. and Paules,R.S. (2001) Assessing gene significance from cdna microarray expression data via mixed models. J. Comput. Biol., 8, 625-637.