-
1
-
-
0001677717
-
Controlling the false discovery rate: A practical and powerful approach to multiple testing
-
Benjamini, Y. and Y. Hochberg (1995): .Controlling the false discovery rate: A practical and powerful approach to multiple testing,. Journal of the Royal Statistical Society B, 57, 289-300.
-
(1995)
Journal of the Royal Statistical Society B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
2
-
-
1842507530
-
Degrees of differential gene expression: Detecting biologically signi.cant expression differences and estimating their magni-tudes
-
(Oxford, England)
-
Bickel, D. R. (2004a): .Degrees of differential gene expression: Detecting biologically signi.cant expression differences and estimating their magni-tudes,.Bioinformatics (Oxford, England), 20, 682-688.
-
(2004)
Bioinformatics
, vol.20
, pp. 682-688
-
-
Bickel, D.R.1
-
3
-
-
14644402541
-
Error-rate and decision-theoretic methods of mul-tiple testing: Which genes have high objective probabilities of differential expression?
-
Bickel, D. R. (2004b): .Error-rate and decision-theoretic methods of mul-tiple testing: Which genes have high objective probabilities of differential expression?. Statistical Applications in Genetics and Molecular Biology, 3, 8.
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
, pp. 8
-
-
Bickel, D.R.1
-
4
-
-
16344387892
-
Probabilities of spurious connections in gene net-works: Application to expression time series
-
(Oxford, Eng-land)
-
Bickel, D. R. (2005): .Probabilities of spurious connections in gene net-works: Application to expression time series,.Bioinformatics (Oxford, Eng-land), 21, 1121-1128.
-
(2005)
Bioinformatics
, vol.21
, pp. 1121-1128
-
-
Bickel, D.R.1
-
5
-
-
48849110493
-
Correcting the estimated level of differential expres-sion for gene selection bias: Application to a microarray study
-
Bickel, D. R. (2008a): .Correcting the estimated level of differential expres-sion for gene selection bias: Application to a microarray study,.Statistical Applications in Genetics and Molecular Biology, 7, 10.
-
(2008)
Statistical Applications in Genetics and Molecular Biology
, vol.7
, pp. 10
-
-
Bickel, D.R.1
-
6
-
-
77949529030
-
The strength of statistical evidence for composite hypotheses with an application to multiple comparisons
-
Ottawa Institute of Systems Biology, COBRA Preprint Series, Article 49, available at tinyurl.com/7yaysp
-
Bickel, D. R. (2008b): .The strength of statistical evidence for composite hypotheses with an application to multiple comparisons,.Technical Report, Ottawa Institute of Systems Biology, COBRA Preprint Series, Article 49, available at tinyurl.com/7yaysp.
-
(2008)
Technical Report
-
-
Bickel, D.R.1
-
7
-
-
77954394077
-
Estimating the null distribution for conditional in-ference and genome-scale screening
-
Ottawa Institute of Systems Biology, arXiv: 0910.0745
-
Bickel, D. R. (2009): .Estimating the null distribution for conditional in-ference and genome-scale screening,.Technical Report, Ottawa Institute of Systems Biology, arXiv:0910.0745.
-
(2009)
Technical Report
-
-
Bickel, D.R.1
-
8
-
-
36749032690
-
Tail posterior probability for in-ference in pairwise and multiclass gene expression data
-
Bochkina, N. and S. Richardson (2007): .Tail posterior probability for in-ference in pairwise and multiclass gene expression data,. Biometrics, 63, 1117-1125.
-
(2007)
Biometrics
, vol.63
, pp. 1117-1125
-
-
Bochkina, N.1
Richardson, S.2
-
9
-
-
34248532878
-
Selection of dif-ferentially expressed genes in microarray data analysis
-
Chen, J. J., S. J. Wang, C. A. Tsai, and C. J. Lin (2007): .Selection of dif-ferentially expressed genes in microarray data analysis,.Pharmacogenomics Journal, 7, 212-220.
-
(2007)
Pharmacogenomics Journal
, vol.7
, pp. 212-220
-
-
Chen, J.J.1
Wang, S.J.2
Tsai, C.A.3
Lin, C.J.4
-
10
-
-
0018324902
-
Association of juvenile disciform maculopathy with hla b15
-
Craandijk, A. and G. M. T. Schreuder (1979): .Association of juvenile disciform maculopathy with hla b15,. British Journal of Ophthalmology, 63, 678-679.
-
(1979)
British Journal of Ophthalmology
, vol.63
, pp. 678-679
-
-
Craandijk, A.1
Schreuder, G.M.T.2
-
11
-
-
42249087793
-
Estimation of significance thresh-olds for genomewide association scans
-
Dudbridge, F. and A. Gusnanto (2008): .Estimation of significance thresh-olds for genomewide association scans,.Genetic Epidemiology, 32, 227-234.
-
(2008)
Genetic Epidemiology
, vol.32
, pp. 227-234
-
-
Dudbridge, F.1
Gusnanto, A.2
-
12
-
-
0043203327
-
Multiple hypothesis testing in microarray experiments
-
DOI 10.1214/ss/1056397487
-
Dudoit, S., J. P. Shaffer, and J. C. Boldrick (2003): .Multiple hypothesis testing in microarray experiments,.Statistical Science, 18, 71-103. (Pubitemid 41461823)
-
(2003)
Statistical Science
, vol.18
, Issue.1
, pp. 71-103
-
-
Dudoit, S.1
Shaffer, J.P.2
Boldrick, J.C.3
-
13
-
-
0002344794
-
Bootstrap methods: Another look at the jackknife
-
Efron, B. (1979): .Bootstrap methods: Another look at the jackknife,.The Annals of Statistics, 7, 1-26.
-
(1979)
The Annals of Statistics
, vol.7
, pp. 1-26
-
-
Efron, B.1
-
14
-
-
2142732441
-
Large-scale simultaneous hypothesis testing: The choice of a null hypothesis
-
Efron, B. (2004): .Large-scale simultaneous hypothesis testing: The choice of a null hypothesis,.Journal of the American Statistical Association, 99, 96-104.
-
(2004)
Journal of the American Statistical Association
, vol.99
, pp. 96-104
-
-
Efron, B.1
-
15
-
-
0035992248
-
Empirical bayes methods and false discovery rates for microarrays
-
Efron, B. and R. Tibshirani (2002): .Empirical bayes methods and false discovery rates for microarrays,.Genetic epidemiology, 23, 70-86.
-
(2002)
Genetic Epidemiology
, vol.23
, pp. 70-86
-
-
Efron, B.1
Tibshirani, R.2
-
16
-
-
1542784653
-
Empirical bayes analysis of a microarray experiment
-
Efron, B., R. Tibshirani, J. D. Storey, and V. Tusher (2001): .Empirical bayes analysis of a microarray experiment,.J. Am. Stat. Assoc., 96, 1151-1160.
-
(2001)
J. Am. Stat. Assoc.
, vol.96
, pp. 1151-1160
-
-
Efron, B.1
Tibshirani, R.2
Storey, J.D.3
Tusher, V.4
-
19
-
-
10844295316
-
-
June 2-6 2002, Oxford: Oxford University Press, chapter Bayesian and frequentist multiple testing
-
Genovese, C. and L. Wasserman (2003): Bayesian Statistics 7: Proceedings of the Seventh Valencia International Meeting, June 2-6, 2002, Oxford: Oxford University Press, chapter Bayesian and frequentist multiple testing, 145-161.
-
(2003)
Bayesian Statistics 7: Proceedings of the Seventh Valencia International Meeting
, pp. 145-161
-
-
Genovese, C.1
Wasserman, L.2
-
20
-
-
33845495923
-
Shrunken p-values for assessing differential expression with applications to genomic data analysis
-
Ghosh, D. (2006): .Shrunken p-values for assessing differential expression with applications to genomic data analysis,.Biometrics, 62, 1099-1106.
-
(2006)
Biometrics
, vol.62
, pp. 1099-1106
-
-
Ghosh, D.1
-
21
-
-
64549126029
-
Empirical bayes methods for estimation and con.dence intervals in high-dimensional problems
-
Ghosh, D. (2009): .Empirical bayes methods for estimation and con.dence intervals in high-dimensional problems,.Statistica Sinica, 19, 125-143.
-
(2009)
Statistica Sinica
, vol.19
, pp. 125-143
-
-
Ghosh, D.1
-
22
-
-
33748495591
-
Rat toxicogenomic study reveals analytical consistency across microarray platforms
-
Guo, L., E. K. Lobenhofer, C. Wang, R. Shippy, S. C. Harris, L. Zhang, N. Mei, T. Chen, D. Herman, F. M. Goodsaid, P. Hurban, K. L. Phillips, J. Xu, X. Deng, Y. A. Sun, W. Tong, Y. P. Dragan, and L. Shi (2006): .Rat toxicogenomic study reveals analytical consistency across microarray platforms,.Nat Biotech, 24, 1162-1169.
-
(2006)
Nat Biotech
, vol.24
, pp. 1162-1169
-
-
Guo, L.1
Lobenhofer, E.K.2
Wang, C.3
Shippy, R.4
Harris, S.C.5
Zhang, L.6
Mei, N.7
Chen, T.8
Herman, D.9
Goodsaid, F.M.10
Hurban, P.11
Phillips, K.L.12
Xu, J.13
Deng, X.14
Sun, Y.A.15
Tong, W.16
Dragan, Y.P.17
Shi, L.18
-
23
-
-
25444435409
-
Fold-change estimation of differentially expressed genes using mixture mixed-model
-
Gusnanto, A., A. Ploner, and Y. Pawitan (2005): .Fold-change estimation of differentially expressed genes using mixture mixed-model,.Statistical Ap-plications in Genetics and Molecular Biology, 4, i.22.
-
(2005)
Statistical Ap-plications in Genetics and Molecular Biology
, vol.4
-
-
Gusnanto, A.1
Ploner, A.2
Pawitan, Y.3
-
24
-
-
58149359201
-
Empirical bayes confidence intervals shrinking both means and variances
-
Hwang, J. T. G., J. Qiu, and Z. Zhao (2009): .Empirical bayes confidence intervals shrinking both means and variances,.Journal of the Royal Statis-tical Society. Series B: Statistical Methodology, 71, 265-285.
-
(2009)
Journal of the Royal Statis-tical Society. Series B: Statistical Methodology
, vol.71
, pp. 265-285
-
-
Hwang, J.T.G.1
Qiu, J.2
Zhao, Z.3
-
25
-
-
0042744696
-
Detecting differentially expressed genes in microarrays using bayesian model selection
-
Ishwaran, H. and J. S. Rao (2003): .Detecting differentially expressed genes in microarrays using bayesian model selection,. Journal of the American Statistical Association, 98, 438-455.
-
(2003)
Journal of the American Statistical Association
, vol.98
, pp. 438-455
-
-
Ishwaran, H.1
Rao, J.S.2
-
26
-
-
0035733752
-
The contributions of sex, genotype and age to transcriptional variance in drosophila melanogaster
-
Jin, W., R. M. Riley, R. D. Wolfinger, K. P. White, G. Passador-Gurgell, and G. Gibson (2001): .The contributions of sex, genotype and age to transcriptional variance in drosophila melanogaster,.Nature Genetics, 29, 389-395.
-
(2001)
Nature Genetics
, vol.29
, pp. 389-395
-
-
Jin, W.1
Riley, R.M.2
Wolfinger, R.D.3
White, K.P.4
Passador-Gurgell, G.5
Gibson, G.6
-
27
-
-
2942651196
-
Modeling microarray data using a threshold mixture model
-
Kauermann, G. and P. Eilers (2004): .Modeling microarray data using a threshold mixture model,.Biometrics, 60, 376-387.
-
(2004)
Biometrics
, vol.60
, pp. 376-387
-
-
Kauermann, G.1
Eilers, P.2
-
28
-
-
0034927555
-
Analysis of variance for gene expression microarray data
-
Kerr, M. K., M. Martin, and G. A. Churchill (2001): .Analysis of variance for gene expression microarray data,.Journal of Computational Biology, 7, 819-837.
-
(2001)
Journal of Computational Biology
, vol.7
, pp. 819-837
-
-
Kerr, M.K.1
Martin, M.2
Churchill, G.A.3
-
29
-
-
33645059429
-
Bayesian modeling of differential gene expression
-
Lewin, A., S. Richardson, C. Marshall, A. Glazier, and T. Aitman (2006): .Bayesian modeling of differential gene expression,.Biometrics, 62, 1-9.
-
(2006)
Biometrics
, vol.62
, pp. 1-9
-
-
Lewin, A.1
Richardson, S.2
Marshall, C.3
Glazier, A.4
Aitman, T.5
-
30
-
-
25144456446
-
Estimating the proportion of true hypotheses, with application to dnamicroarray data
-
M. Langaas, B. H. L. and E. Ferkingstad (2005): .Estimating the proportion of true hypotheses, with application to dna microarray data,. Journal of the Royal Statistical Society. B, 67.
-
(2005)
Journal of the Royal Statistical Society. B
, pp. 67
-
-
Langaas, M.1
Ferkingstad, E.2
-
31
-
-
57249083246
-
Frequentist statistics as a theory of inductive inference
-
The Second Erich L. Lehmann Symposium - Optimality.
-
Mayo, D. G. and D. R. Cox (2006): .Frequentist statistics as a theory of inductive inference,. IMS Lecture Notes -Monograph Series, The Second Erich L. Lehmann Symposium -Optimality.
-
(2006)
IMS Lecture Notes -Monograph Series
-
-
Mayo, D.G.1
Cox, D.R.2
-
32
-
-
62549109118
-
Testing significance relative to a fold-change threshold is a treat
-
(Oxford, England)
-
McCarthy, D. J. and G. K. Smyth (2009a): .Testing significance relative to a fold-change threshold is a treat,.Bioinformatics (Oxford, England), 25, 765-771.
-
(2009)
Bioinformatics
, vol.25
, pp. 765-771
-
-
McCarthy, D.J.1
Smyth, G.K.2
-
33
-
-
62549109118
-
Testing significance relative to a fold-change threshold is a TREAT
-
McCarthy, D. J. and G. K. Smyth (2009b): .Testing significance relative to a fold-change threshold is a TREAT,.Bioinformatics, 25, 765-771.
-
(2009)
Bioinformatics
, vol.25
, pp. 765-771
-
-
McCarthy, D.J.1
Smyth, G.K.2
-
35
-
-
4444235995
-
Detect-ing differential gene expression with a semiparametric hierarchical mixture method
-
Newton, M. A., A. Noueiry, D. Sarkar, and P. Ahlquist (2004): .Detect-ing differential gene expression with a semiparametric hierarchical mixture method,.Biostatistics, 5, 155-176.
-
(2004)
Biostatistics
, vol.5
, pp. 155-176
-
-
Newton, M.A.1
Noueiry, A.2
Sarkar, D.3
Ahlquist, P.4
-
36
-
-
5344244656
-
-
R Development Core Team, Vienna, Austria: R Foundation for Statistical Com-puting
-
R Development Core Team (2008): R: A language and environment for statistical computing, Vienna, Austria: R Foundation for Statistical Com-puting.
-
(2008)
R: A Language and Environment for Statistical Computing
-
-
-
37
-
-
23744484462
-
Analyzing factorial designed microarray experiments
-
Scholtens, D., A. Miron, F. M. Merchant, A. Miller, P. L. Miron, J. D. Igle-hart, and R. Gentleman (2004): .Analyzing factorial designed microarray experiments,.J. Multivar. Anal., 90, 19-43.
-
(2004)
J. Multivar. Anal.
, vol.90
, pp. 19-43
-
-
Scholtens, D.1
Miron, A.2
Merchant, F.M.3
Miller, A.4
Miron, P.L.5
Igle-Hart, J.D.6
Gentleman, R.7
-
38
-
-
27844521293
-
A shrinkage approach to large-scale co-variance matrix estimation and implications for functional genomics
-
Schäfer, J. and K. Strimmer (2005): .A shrinkage approach to large-scale co-variance matrix estimation and implications for functional genomics,.Sta-tistical Applications in Genetics and Molecular Biology, 4, 1-30.
-
(2005)
Sta-tistical Applications in Genetics and Molecular Biology
, vol.4
, pp. 1-30
-
-
Schäfer, J.1
Strimmer, K.2
-
40
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Smyth, G. K. (2004): .Linear models and empirical bayes methods for assessing differential expression in microarray experiments,.Statistical Ap-plications in Genetics and Molecular Biology, 3.
-
(2004)
Statistical Ap-plications in Genetics and Molecular Biology
, vol.3
-
-
Smyth, G.K.1
-
41
-
-
17644422198
-
Reduction of selection bias in genomewide studies by resampling
-
Sun, L. and S. B. Bull (2005): .Reduction of selection bias in genomewide studies by resampling,.Genetic Epidemiology, 28, 352-367.
-
(2005)
Genetic Epidemiology
, vol.28
, pp. 352-367
-
-
Sun, L.1
Bull, S.B.2
-
42
-
-
33747595466
-
Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies
-
Sun, L., R. V. Craiu, A. D. Paterson, and S. B. Bull (2006): .Stratified false discovery control for large-scale hypothesis testing with application to genome-wide association studies,.Genetic Epidemiology, 30, 519-530.
-
(2006)
Genetic Epidemiology
, vol.30
, pp. 519-530
-
-
Sun, L.1
Craiu, R.V.2
Paterson, A.D.3
Bull, S.B.4
-
43
-
-
33745603720
-
A markov chain monte carlo version of the genetic algorithm differential evolution: Easy bayesian computing for real parameter spaces
-
Ter Braak, C. J. F. (2006): .A markov chain monte carlo version of the genetic algorithm differential evolution: easy bayesian computing for real parameter spaces,.Statistics and Computing, 16, 239-249.
-
(2006)
Statistics and Computing
, vol.16
, pp. 239-249
-
-
Ter Braak, C.J.F.1
-
44
-
-
0035681150
-
Bayesian estimation of fold-changes in the analysis of gene expression: The pfold algorithm
-
Theilhaber, J., S. Bushnell, A. Jackson, and R. Fuchs (2001): .Bayesian estimation of fold-changes in the analysis of gene expression: The pfold algorithm,.Journal of Computational Biology, 8, 585-614.
-
(2001)
Journal of Computational Biology
, vol.8
, pp. 585-614
-
-
Theilhaber, J.1
Bushnell, S.2
Jackson, A.3
Fuchs, R.4
-
46
-
-
34548456099
-
Estimating the false discovery rate using nonparametric deconvolution
-
Van De Wiel, M. A. and K. I. Kim (2007): .Estimating the false discovery rate using nonparametric deconvolution,.Biometrics, 63, 806-815.
-
(2007)
Biometrics
, vol.63
, pp. 806-815
-
-
Van De Wiel, M.A.1
Kim, K.I.2
-
47
-
-
0000217080
-
Gene expression analysis with the parametric bootstrap
-
Van Der Laan, M. J. and J. Bryan (2001): .Gene expression analysis with the parametric bootstrap,.Biostat, 2, 445-461.
-
(2001)
Biostat
, vol.2
, pp. 445-461
-
-
Van Der Laan, M.J.1
Bryan, J.2
-
48
-
-
14644413619
-
Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives
-
Van der Laan, M. J., S. Dudoit, and K. S. Pollard (2004): .Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives,. Stat. Appl. in Genet. and Mol. Biol., 3, 15.
-
(2004)
Stat. Appl. in Genet. and Mol. Biol.
, vol.3
, pp. 15
-
-
Van Der Laan, M.J.1
Dudoit, S.2
Pollard, K.S.3
-
49
-
-
59149090877
-
Shrinkage confidence intervals for the normal mean: Using a guess for greater efficiency
-
Willink, R. (2008): .Shrinkage confidence intervals for the normal mean: using a guess for greater efficiency,.The Canadian Journal of Statistics, 34, 623-637.
-
(2008)
The Canadian Journal of Statistics
, vol.34
, pp. 623-637
-
-
Willink, R.1
-
50
-
-
77949495872
-
Validation of differential gene expression algorithms: Application comparing fold-change estimation to hy-pothesis testing
-
Yanofsky, C. M. and D. R. Bickel (2010): .Validation of differential gene expression algorithms: Application comparing fold-change estimation to hy-pothesis testing,.BMC Bioinformatics, 11, 63.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 63
-
-
Yanofsky, C.M.1
Bickel, D.R.2
|