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Volumn 12, Issue SUPPL. 5, 2011, Pages

A gene selection method for GeneChip array data with small sample sizes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FALSE DISCOVERY RATE; FALSE POSITIVE RESULT; INTERMETHOD COMPARISON; MICROARRAY ANALYSIS; MODEL BASED INFORMATION SHARING METHOD; NORMAL DISTRIBUTION; RECEIVER OPERATING CHARACTERISTIC; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; SIMULATION; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; STUDENT T TEST; ALGORITHM; BIOLOGICAL MODEL; DNA MICROARRAY;

EID: 84255175726     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-S5-S7     Document Type: Article
Times cited : (8)

References (34)
  • 2
    • 0035942271 scopus 로고    scopus 로고
    • Significance analysis of microarrays applied to the ionizing radiation response
    • 10.1073/pnas.091062498, 33173, 11309499
    • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 2001, 98(9):5116-5121. 10.1073/pnas.091062498, 33173, 11309499.
    • (2001) Proc Natl Acad Sci USA , vol.98 , Issue.9 , pp. 5116-5121
    • Tusher, V.G.1    Tibshirani, R.2    Chu, G.3
  • 3
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: a practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Statist Soc B 1995, 57:289-300.
    • (1995) J R Statist Soc B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 4
    • 0036020892 scopus 로고    scopus 로고
    • A direct approach to false discovery rates
    • Storey J. A direct approach to false discovery rates. J R Statist Soc B 2002, 64:479-498.
    • (2002) J R Statist Soc B , vol.64 , pp. 479-498
    • Storey, J.1
  • 5
    • 0042424602 scopus 로고    scopus 로고
    • Statistical significance for genomewide studies
    • 10.1073/pnas.1530509100, 170937, 12883005
    • Storey JD, Tibshirani R. Statistical significance for genomewide studies. Proc Natl Acad Sci USA 2003, 100(16):9440-9445. 10.1073/pnas.1530509100, 170937, 12883005.
    • (2003) Proc Natl Acad Sci USA , vol.100 , Issue.16 , pp. 9440-9445
    • Storey, J.D.1    Tibshirani, R.2
  • 6
    • 4444294164 scopus 로고    scopus 로고
    • Improving false discovery rate estimation
    • 10.1093/bioinformatics/bth160, 14988112
    • Pounds S, Cheng C. Improving false discovery rate estimation. Bioinformatics 2004, 20(11):1737-1745. 10.1093/bioinformatics/bth160, 14988112.
    • (2004) Bioinformatics , vol.20 , Issue.11 , pp. 1737-1745
    • Pounds, S.1    Cheng, C.2
  • 7
    • 17444374677 scopus 로고    scopus 로고
    • Differential gene expression detection using penalized linear regression models: the improved SAM statistics
    • 10.1093/bioinformatics/bti217, 15598833
    • Wu B. Differential gene expression detection using penalized linear regression models: the improved SAM statistics. Bioinformatics 2005, 21:1565-1571. 10.1093/bioinformatics/bti217, 15598833.
    • (2005) Bioinformatics , vol.21 , pp. 1565-1571
    • Wu, B.1
  • 8
    • 33845913494 scopus 로고    scopus 로고
    • Estimating p-values in small microarray experiments
    • 10.1093/bioinformatics/btl548, 17077100
    • Yang H, Churchill G. Estimating p-values in small microarray experiments. Bioinformatics 2007, 23(1):38-43. 10.1093/bioinformatics/btl548, 17077100.
    • (2007) Bioinformatics , vol.23 , Issue.1 , pp. 38-43
    • Yang, H.1    Churchill, G.2
  • 9
    • 33645024314 scopus 로고    scopus 로고
    • Assessing stability of gene selection in microarray data analysis
    • 10.1186/1471-2105-7-50, 1403808, 16451725
    • Qiu X, Xiao Y, Gordon A, Yakovlev A. Assessing stability of gene selection in microarray data analysis. BMC Bioinformatics 2006, 7:50. 10.1186/1471-2105-7-50, 1403808, 16451725.
    • (2006) BMC Bioinformatics , vol.7 , pp. 50
    • Qiu, X.1    Xiao, Y.2    Gordon, A.3    Yakovlev, A.4
  • 10
    • 84870816675 scopus 로고    scopus 로고
    • Bioconductor
    • Bioconductor. , http://www.bioconductor.org
  • 11
    • 1142273091 scopus 로고    scopus 로고
    • Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach
    • Storey J, Taylor JE, Siegmund D. Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach. J R Stat Soc B 2004, 66:87-205.
    • (2004) J R Stat Soc B , vol.66 , pp. 87-205
    • Storey, J.1    Taylor, J.E.2    Siegmund, D.3
  • 12
    • 33747877325 scopus 로고    scopus 로고
    • How accurately can we control the FDR in analyzing microarray data?
    • 10.1093/bioinformatics/btl161, 16644791
    • Jung S, Jang W. How accurately can we control the FDR in analyzing microarray data?. Bioinformatics 2006, 22:1730-1736. 10.1093/bioinformatics/btl161, 16644791.
    • (2006) Bioinformatics , vol.22 , pp. 1730-1736
    • Jung, S.1    Jang, W.2
  • 13
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • 10.1126/science.278.5338.680, 9381177
    • DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278(5338):680-686. 10.1126/science.278.5338.680, 9381177.
    • (1997) Science , vol.278 , Issue.5338 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 14
    • 0029748326 scopus 로고    scopus 로고
    • Parallel human genome analysis: microarray-based expression monitoring of 1000 genes
    • 10.1073/pnas.93.20.10614, 38202, 8855227
    • Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 1996, 93(20):10614-10619. 10.1073/pnas.93.20.10614, 38202, 8855227.
    • (1996) Proc Natl Acad Sci USA , vol.93 , Issue.20 , pp. 10614-10619
    • Schena, M.1    Shalon, D.2    Heller, R.3    Chai, A.4    Brown, P.O.5    Davis, R.W.6
  • 15
    • 20844440189 scopus 로고    scopus 로고
    • Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates
    • 10.1093/bioinformatics/bti413, 15814562
    • Chen DT, Chen JJ, Soong SJ. Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates. Bioinformatics 2005, 21(12):2861-2866. 10.1093/bioinformatics/bti413, 15814562.
    • (2005) Bioinformatics , vol.21 , Issue.12 , pp. 2861-2866
    • Chen, D.T.1    Chen, J.J.2    Soong, S.J.3
  • 16
    • 33847288899 scopus 로고    scopus 로고
    • A distribution free summarization method for Affymetrix GeneChip arrays
    • 10.1093/bioinformatics/btl609, 17148508
    • Chen Z, McGee M, Liu Q, Scheuermann RH. A distribution free summarization method for Affymetrix GeneChip arrays. Bioinformatics 2007, 23(3):321-327. 10.1093/bioinformatics/btl609, 17148508.
    • (2007) Bioinformatics , vol.23 , Issue.3 , pp. 321-327
    • Chen, Z.1    McGee, M.2    Liu, Q.3    Scheuermann, R.H.4
  • 17
    • 38849106351 scopus 로고    scopus 로고
    • A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments
    • 10.1093/bioinformatics/btm620, 18204063
    • Hong F, Breitling R. A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics 2008, 24(3):374-382. 10.1093/bioinformatics/btm620, 18204063.
    • (2008) Bioinformatics , vol.24 , Issue.3 , pp. 374-382
    • Hong, F.1    Breitling, R.2
  • 18
    • 32544432046 scopus 로고    scopus 로고
    • Comparison of various statistical methods for identifying differential gene expression in replicated microarray data
    • 10.1191/0962280206sm423oa, 16477945
    • Kim S, Lee J, Sohn I. Comparison of various statistical methods for identifying differential gene expression in replicated microarray data. Stat Methods Med Res 2006, 15:3-20. 10.1191/0962280206sm423oa, 16477945.
    • (2006) Stat Methods Med Res , vol.15 , pp. 3-20
    • Kim, S.1    Lee, J.2    Sohn, I.3
  • 19
    • 27744579507 scopus 로고    scopus 로고
    • An expression index for Affymetrix GeneChips based on the generalized logarithm
    • 10.1093/bioinformatics/bti665, 16159924
    • Zhou L, Rocke DM. An expression index for Affymetrix GeneChips based on the generalized logarithm. Bioinformatics 2005, 21(21):3983-3989. 10.1093/bioinformatics/bti665, 16159924.
    • (2005) Bioinformatics , vol.21 , Issue.21 , pp. 3983-3989
    • Zhou, L.1    Rocke, D.M.2
  • 20
    • 0012572299 scopus 로고    scopus 로고
    • A variance-stabilizing transformation for gene-expression microarray data
    • 10.1093/bioinformatics/18.suppl_1.S105, 12169537
    • Durbin BP, Hardin JS, Hawkins DM, Rocke DM. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002, 18(Suppl 1):S105-110. 10.1093/bioinformatics/18.suppl_1.S105, 12169537.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Durbin, B.P.1    Hardin, J.S.2    Hawkins, D.M.3    Rocke, D.M.4
  • 21
    • 11244346557 scopus 로고    scopus 로고
    • Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    • 10.1093/bioinformatics/18.suppl_1.S96, 12169536
    • Huber W, von Heydebreck A, Sultmann H, Poustka A, Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 2002, 18(Suppl 1):S96-104. 10.1093/bioinformatics/18.suppl_1.S96, 12169536.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Huber, W.1    von Heydebreck, A.2    Sultmann, H.3    Poustka, A.4    Vingron, M.5
  • 22
    • 33749861279 scopus 로고    scopus 로고
    • Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
    • 10.1093/bioinformatics/btl412, 16877753
    • Motakis ES, Nason GP, Fryzlewicz P, Rutter GA. Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach. Bioinformatics 2006, 22(20):2547-2553. 10.1093/bioinformatics/btl412, 16877753.
    • (2006) Bioinformatics , vol.22 , Issue.20 , pp. 2547-2553
    • Motakis, E.S.1    Nason, G.P.2    Fryzlewicz, P.3    Rutter, G.A.4
  • 23
    • 0035684378 scopus 로고    scopus 로고
    • A model for measurement error for gene expression arrays
    • 10.1089/106652701753307485, 11747612
    • Rocke DM, Durbin B. A model for measurement error for gene expression arrays. J Comput Biol 2001, 8(6):557-569. 10.1089/106652701753307485, 11747612.
    • (2001) J Comput Biol , vol.8 , Issue.6 , pp. 557-569
    • Rocke, D.M.1    Durbin, B.2
  • 24
  • 25
    • 84888000943 scopus 로고    scopus 로고
    • NCBI GEO Database
    • NCBI GEO Database. , http://www.ncbi.nih.gov/projects/geo
  • 26
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • 10.1093/bioinformatics/19.2.185, 12538238
    • 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. 10.1093/bioinformatics/19.2.185, 12538238.
    • (2003) Bioinformatics , vol.19 , Issue.2 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 27
    • 84855854915 scopus 로고    scopus 로고
    • CLASSIFI
    • CLASSIFI. , http://pathcuric1.swmed.edu/pathdb/classifi.html
  • 29
    • 33745062476 scopus 로고    scopus 로고
    • Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
    • 10.1186/1471-2105-7-237, 1479375, 16670020
    • Lee JA, Sinkovits RS, Mock D, Rab EL, Cai J, Yang P, Saunders B, Hsueh RC, Choi S, Subramaniam S, Scheuermann RH. Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics 2006, 7:237. 10.1186/1471-2105-7-237, 1479375, 16670020.
    • (2006) BMC Bioinformatics , vol.7 , pp. 237
    • Lee, J.A.1    Sinkovits, R.S.2    Mock, D.3    Rab, E.L.4    Cai, J.5    Yang, P.6    Saunders, B.7    Hsueh, R.C.8    Choi, S.9    Subramaniam, S.10    Scheuermann, R.H.11
  • 30
    • 0034887203 scopus 로고    scopus 로고
    • Creating the gene ontology resource: design and implementation
    • 10.1101/gr.180801, 311077, 11483584, The Gene Ontology Consortium
    • The Gene Ontology Consortium Creating the gene ontology resource: design and implementation. Genome Res 2001, 11(8):1425-1433. 10.1101/gr.180801, 311077, 11483584, The Gene Ontology Consortium.
    • (2001) Genome Res , vol.11 , Issue.8 , pp. 1425-1433
  • 31
    • 67650556407 scopus 로고    scopus 로고
    • A distribution-free convolution model for background correction of oligonucleotide microarray data
    • 10.1186/1471-2164-10-S1-S19, 2788371, 19958482
    • Chen Z, McGee M, Liu Q, Kong M, Deng Y, Scheuermann RH. A distribution-free convolution model for background correction of oligonucleotide microarray data. BMC Genomics 2009, 10(Suppl 1):S19. 10.1186/1471-2164-10-S1-S19, 2788371, 19958482.
    • (2009) BMC Genomics , vol.10 , Issue.SUPPL. 1
    • Chen, Z.1    McGee, M.2    Liu, Q.3    Kong, M.4    Deng, Y.5    Scheuermann, R.H.6
  • 32
    • 78651398270 scopus 로고    scopus 로고
    • Identifying differentially expressed genes based on probe level data for GeneChip arrays
    • 10.1504/IJCBDD.2010.038028, 21228458
    • Chen Z, McGee M, Liu Q, Kong YM, Huang X, Yang JY, Scheuermann RH. Identifying differentially expressed genes based on probe level data for GeneChip arrays. Int J Comput Biol Drug Des 2010, 3(3):237-257. 10.1504/IJCBDD.2010.038028, 21228458.
    • (2010) Int J Comput Biol Drug Des , vol.3 , Issue.3 , pp. 237-257
    • Chen, Z.1    McGee, M.2    Liu, Q.3    Kong, Y.M.4    Huang, X.5    Yang, J.Y.6    Scheuermann, R.H.7
  • 33
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • 10.1093/biostatistics/4.2.249, 12925520
    • 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. 10.1093/biostatistics/4.2.249, 12925520.
    • (2003) Biostatistics , vol.4 , Issue.2 , pp. 249-264
    • Irizarry, R.A.1    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5    Scherf, U.6    Speed, T.P.7
  • 34
    • 33749027459 scopus 로고    scopus 로고
    • Parameter estimation for the exponential-normal convolution model for background correction of affymetrix GeneChip data
    • McGee M, Chen Z. Parameter estimation for the exponential-normal convolution model for background correction of affymetrix GeneChip data. Stat Appl Genet Mol Biol 2006, 5:Article24.
    • (2006) Stat Appl Genet Mol Biol , vol.5
    • McGee, M.1    Chen, Z.2


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