A comparison of statistical tests for detecting differential expression using Affymetrix oligonucleotide microarrays

OMICS A Journal of Integrative Biology

Volumn 10, Issue 4, 2006, Pages 555-566

  Vardhanabhuti, Saran ^a   Blakemore, Steven J ^b   Clark, Steven M ^b   Ghosh, Sujoy ^b   Stephens, Richard J ^c   Rajagopalan, Dilip ^b  

^a ROSETTA INPHARMATICS   (United States)

^b GLAXOSMITHKLINE   (United States)

^c GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE;

ALGORITHM; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DNA DETERMINATION; DNA MICROARRAY; EVALUATION; GENE EXPRESSION; INFORMATION PROCESSING; INTERMETHOD COMPARISON; LIVER; METHODOLOGY; MICROARRAY ANALYSIS; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RAT; ROC CURVE; SIGNAL DETECTION; STATISTICAL ANALYSIS; STATISTICAL PARAMETERS; STUDENT T TEST; TRANSCRIPTOMICS;

ANIMALS; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

RATTUS RATTUS;

EID: 33846617322     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/omi.2006.10.555     Document Type: Article

References (14)

1. BREITLING, R., ARMENGAUD, P., AMTMANN, A., and HERZYK, P. (2004). Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett 573, 83-92
2. CHOE, S.E., BOUTROS, M., MICHELSON, A.M., CHURCH, G.M. and HALFON, M.S. (2005). Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 6, R16.
3. COPE, L.M., IRIZARRY, R.A., JAFFEE, H., WU, Z., and SPEED, T.P. (2003). A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20, 323-331.
4. HUBER, W., VON HEYDEBRECK, A., SULTMANN, H., POUSTKA, A., and VINGRON, M. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18, S96-S104.
5. 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 Nucl Acids Res 31, e15.
6. JAIN, N., THATTE, J., BRACIALE, T., LEY, K., O'CONNELL, M., and LEE, J.K. (2003). Local-pooled-error test for identifying differentially expressed genes with a small number of replicated microarrays. Bioinformatics 19, 1945-1951.
7. LOCKHART, D.J., DONG, H., BRYNE, M.C., FOLLETTIE, M.T., GALLO, M.V., CHEE, M.S., et al. (1996). Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 14, 1675-1680.
8. LONG, A.D., MANGALAM, H.J., CHAN, B.Y.P., TOLLERI, L., HATFIELD, G.W., and BALDI, P. (2001). Improved statistical inference from DNA microarray Data using analysis of variance and a Bayesian statistical framework. J Biol Chem, 276, 19937-19944.
9. RAJAGOPALAN, D. (2003). A comparison of statistical methods for analysis of high density oligonucleotide array data. Bioinformatics 19, 1469-1476.
10. SHEDDEN, K., CHEN, W., KUICK, R., GHOSH, D., MACDONALD, J., CHO, K.R., et al. (2005). Comparison of seven methods for producing Affymetrix expression scores based on false discovery rates in disease profiling data. BMC Bioinformatics, 6, 26.
11. QIN, L.X., BEYER, R.P., HUDSON, F.N., LINFORD, N.J., MORRIS, D.E., and KERR, K.F. (2006). Evaluation of methods for oligonucleotide array data via quantitative real-time PCR. BMC Bioinformatics 7, 23.
12. TUSHER, V.G., TIBSHIRANI, R., and CHU, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. PNAS 98, 5116-5121.
13. WENG, L., DAI, H., ZHAN, Y., HE, Y., STEPANIANTS, S.B., and BASSETT, D.E. (2006). Rosetta error model for gene expression analysis. Bioinformatics 22, 1111-1121.
14. WU Z., IRIZARRY, R.A., GENTLEMAN, R., MARTINEZ MURILLO, F., and SPENCER, F. (2004). A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 99: 909-917.