Utilization of two sample t-test statistics from redundant probe sets to evaluate different probe set algorithms in GeneChip studies

BMC Bioinformatics

Volumn 7, Issue , 2006, Pages

  Hu, Zihua ^a   Willsky, Gail R ^b  

^a UNIVERSITY AT BUFFALO   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFERENTIALLY EXPRESSED GENE; EXPERIMENTAL METHODS; EXPRESSED GENES; GENE EXPRESSION DATA ANALYSIS; REFERENCE DATA; RELATIVE PERFORMANCE; SET REDUNDANCIES; TWO SAMPLE T TESTS;

GENE EXPRESSION; REDUNDANCY; STATISTICAL TESTS; STATISTICS;

PROBES;

DNA; DNA PROBE;

ANALYSIS OF VARIANCE; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; DNA MICROARRAY; EXPERIMENTAL STUDY; GENE EXPRESSION; GENE PROBE; GENETIC ALGORITHM; NONHUMAN; NUCLEOTIDE SEQUENCE; RAT; REDUNDANCY ANALYSIS; STATISTICAL ANALYSIS; STUDENT T TEST; VALIDATION STUDY; ALGORITHM; BIOLOGICAL MODEL; COMPUTER PROGRAM; DNA PROBE; EVALUATION STUDY; GENE EXPRESSION PROFILING; GENETICS; PROCEDURES; REPRODUCIBILITY; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL;

ALGORITHMS; DATA INTERPRETATION, STATISTICAL; DNA PROBES; GENE EXPRESSION PROFILING; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; SOFTWARE; SOFTWARE VALIDATION;

EID: 33646141149     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-7-12     Document Type: Article

References (28)

1. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL: Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996, 14(13):1675-1680.
2. Schena M, Shalon D, Davis RW, Brown PO: Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995, 270(5235):467-470.
3. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, Wang J, Hsu HC, Mountz JD, Baldwin NE, Langston MA, Threadgill DW, Manly KF, Williams RW: Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genetics 2005, 37(3):233-242.
4. Hunter BG, Beatty MK, Singletary GW, Hamaker BR, Dilkes BP, Larkins BA, Jung R: Maize opaque endosperm mutations create extensive changes in patterns of gene expression. Plant Cell 2002, 14(10):2591-2612.
5. Misson J, Raghothama KG, Jain A, Jouhet J, Block MA, Bligny R, Ortet P, Creff A, Somerville S, Rolland N, Doumas P, Nacry P, Herrerra-Estrella L, Nussaume L, Thibaud MC: A genome-wide transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips determined plant responses to phosphate deprivation. PNAS USA 2005, 102(33):11934 -111939.
6. Aflymetrix [http://www.affymetrix.com/support/technical/ byproduct.affx?product=mas].
7. Li C, Hung Wong W: Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001, 2(8):RESEARCH0032.
8. Li C, Wong WH: Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. PNAS USA 2001, 98(1):31-36.
9. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249-264.
10. Barash Y, Dehan E, Krupsky M, Franklin W, Geraci M, Friedman N, Kaminski N: Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays. Bioinformatics 2004, 20(6):839-846.
11. Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193.
12. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP: Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15.
13. Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP: A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 2004, 20(3):323-331.
14. Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS: Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 2005, 6(2):R16.
15. Affymetrix [http://www.affymetrix.com/support/technical/sample_data/ datasets.affx].
16. Seo J, Bakay M, Chen YW, Hilmer S, Shneiderman B, Hoffman EP: Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics 2004, 20(16):2534-2544.
17. GeneLogic dilution data [http://www.GeneLogic.dilution.com/].
18. Willsky GR, Chi LH, Liang Y, Gaile DP, Hu Z, Crans DC: Diabetes altered gene expression in rat skeletal muscle corrected by oral administration of vanadyl sulfate (submitted).
19. Modrek B, Lee C: A genomic view of alternative splicing. Nat Genet 2002, 30(1):13-19.
20. Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. JRSSB 1995, 57(1):289-300.
21. BDGP Drosophila gene collection [http://www.pubmedcentral.gov/ redirect3.cgi?&&reftype=extlink&artid=551536&iid= 18399&jid=7&&http://www.fruitfly.org/DGC/index.html].
22. Affymetrix [http://www.affymetrix.com/].
23. Dennis GJ, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA: DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol 2003, 4(5):P3.
24. Saltiel AR, Kahn CR: Insulin signalling and the regulation of glucose and lipid metabolism. Nature 2001, 414(6865):799-806.
25. Yechoor VK, Patti ME, Saccone R, Kahn CR: Coordinated patterns of gene expression for substrate and energy metabolism in skeletal muscle of diabetic mice. PNAS USA 2002, 99(16):10587-10592.
26. Harbig J, Sprinkle R, Enkemann SA: A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array. Nucleic Acids Res 2005, 33(3):e31.
27. dChip software [http://biosunl.harvard.edu/complab/dchip/]
28. Bioconductor [http://www.bioconductor.org/].