-
1
-
-
0036900895
-
Fundamentals of experimental design for cdna microarrays
-
G.A. Churchill. Fundamentals of experimental design for cDNA microarrays. Nature Genetics 32 (Suppl): 490-495, 2002.
-
(2002)
Nature Genetics
, vol.32
, pp. 490-495
-
-
Churchill, G.A.1
-
3
-
-
0034992423
-
Experimental design, analysis of variance and slide quality assessment in gene expression arrays
-
S. Draghici, A. Kuklin, B. Hoff, and S. Shams. Experimental design, analysis of variance and slide quality assessment in gene expression arrays. Current Opinion in Drug Discovery and Development 4: 332-337, 2001.
-
(2001)
Current Opinion in Drug Discovery and Development
, vol.4
, pp. 332-337
-
-
Draghici, S.1
Kuklin, A.2
Hoff, B.3
Shams, S.4
-
4
-
-
0141966130
-
-
Santa Clara, CA; Affymetrix, Inc
-
Affymetrix. Statistical Algorithms Description Document. Santa Clara, CA; Affymetrix, Inc. 2002. http://www.affymetrix.com/support/technical/whitepapers/sadd-whitepaper.pdf.
-
(2002)
Statistical Algorithms Description Document
-
-
-
5
-
-
12244284624
-
Dna microarray experiments: Biological and technological aspects
-
D.V. Nguyen, A.B. Arpat, N. Wang, and R.J. Carroll. DNA microarray experiments: biological and technological aspects. Biometrics 58: 701-717, 2002.
-
(2002)
Biometrics
, vol.58
, pp. 701-717
-
-
Nguyen, D.V.1
Arpat, A.B.2
Wang, N.3
Carroll, R.J.4
-
6
-
-
0034730124
-
Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cdna hybridizations
-
M.T. Lee, F.C. Kuo, G.A. Whitmore, and J. Sklar. Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proceedings of the National Academy of Sciences, USA 97: 9834-9839, 2000.
-
(2000)
Proceedings of the National Academy of Sciences, USA
, vol.97
, pp. 9834-9839
-
-
Lee, M.T.1
Kuo, F.C.2
Whitmore, G.A.3
Sklar, J.4
-
7
-
-
0034918462
-
Analysis issues for gene expression array data
-
J.K. Lee. Analysis issues for gene expression array data. Clinical Chemistry 47: 1350-1352, 2001.
-
(2001)
Clinical Chemistry
, vol.47
, pp. 1350-1352
-
-
Lee, J.K.1
-
8
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
-
W. Huber, A. von Heydebreck, H. Sultmann, A. Poustka, and M. Vingron. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 (Suppl 1): S96-S104, 2002.
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. SS96-S104
-
-
Huber, W.1
Von Heydebreck, A.2
Sultmann, H.3
Poustka, A.4
Vingron, M.5
-
10
-
-
0043089918
-
Transformation and normalization of oligonucleotide microarray data
-
S.C. Geller, J.P. Gregg, P. Hagerman, and D.M. Rocke. Transformation and normalization of oligonucleotide microarray data. Bioinformatics 19: 1817-1823, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 1817-1823
-
-
Geller, S.C.1
Gregg, J.P.2
Hagerman, P.3
Rocke, D.M.4
-
12
-
-
0035687554
-
Assessing gene significance from cdna microarray expression data via mixed models
-
R.D. Wolfinger, G. Gibson, E.D. Wolfinger, L. Bennett, H. Hamadeh, P. Bushel, C. Afshari, and R.S. Paules. Assessing gene significance from cDNA microarray expression data via mixed models. Journal of Computational Biology 8: 625-637, 2001.
-
(2001)
Journal of Computational Biology
, vol.8
, pp. 625-637
-
-
Wolfinger, R.D.1
Gibson, G.2
Wolfinger, E.D.3
Bennett, L.4
Hamadeh, H.5
Bushel, P.6
Afshari, C.7
Paules, R.S.8
-
14
-
-
3142715303
-
Sources of variation in microarray gene expression data
-
J.J. Chen, R.R. Delongchamp, T. Chen-An, V. Desai, and J. Fuscoe. Sources of variation in microarray gene expression data. Bioinformatics 20: 1436-1446, 2004.
-
(2004)
Bioinformatics
, vol.20
, pp. 1436-1446
-
-
Chen, J.J.1
Delongchamp, R.R.2
Chen-An, T.3
Desai, V.4
Fuscoe, J.5
-
15
-
-
4644233145
-
Microarray gene expression
-
2nd ed., Shein-Chung Chow (ed.), Marcel-Dekker, New York
-
J.J. Chen and C.-H. Chen. Microarray gene expression. In: Encyclopedia of Biopharmaceutical Statistics, 2nd ed., Shein-Chung Chow (ed.), Marcel-Dekker, New York, 2003.
-
(2003)
Encyclopedia of Biopharmaceutical Statistics
-
-
Chen, J.J.1
Chen, C.-H.2
-
16
-
-
0037276175
-
Statistical tests for differential expression in cdna microarray experiments
-
X. Cui and G.A. Churchill. Statistical tests for differential expression in cDNA microarray experiments. Genome Biology 4: 210.1-210.10, 2003.
-
(2003)
Genome Biology
, vol.4
-
-
Cui, X.1
Churchill, G.A.2
-
17
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
C. Li and W.H. Wong. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proceedings of the National Academy of Sciences USA 98: 31-36, 2001.
-
(2001)
Proceedings of the National Academy of Sciences
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
18
-
-
0037287998
-
Normalization methods for analysis of microarray gene-expression data
-
Y.-J. Chen, R. Kodell, F. Sistare, K.L. Thompson, S. Morris, and J.J. Chen. Normalization methods for analysis of microarray gene-expression data. Journal of Biopharmaceutical Statistics 13: 57-74, 2003.
-
(2003)
Journal of Biopharmaceutical Statistics
, vol.13
, pp. 57-74
-
-
Chen, Y.-J.1
Kodell, R.2
Sistare, F.3
Thompson, K.L.4
Morris, S.5
Chen, J.J.6
-
19
-
-
0037316303
-
A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias
-
B.M. Bolstad, R.A. Irizarry, M. Astrand, and T.P. Speed. A comparison of normalization methods for high-density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185-193, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
20
-
-
4644342037
-
Effect of normalization on significance testing for oligonucleotide microarrays
-
R.S. Parrish and H.J. Spencer. Effect of normalization on significance testing for oligonucleotide microarrays. Journal of Biopharmaceutical Statistics 14: 575-589, 2004.
-
(2004)
Journal of Biopharmaceutical Statistics
, vol.14
, pp. 575-589
-
-
Parrish, R.S.1
Spencer, H.J.2
-
21
-
-
0035577641
-
Identification and validation of endogenous reference genes for expression profiling of t helper cell differentiation by quantitative real-time rt-pcr
-
H.K. Hamalainen, J.C. Tubman, S. Vikman, T. Kyrola, E. Ylikoski, J.A. Warrington, and R. Lahesmaa. Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative real-time RT-PCR. Analytical Biochemistry 299: 63-70, 2001.
-
(2001)
Analytical Biochemistry
, vol.299
, pp. 63-70
-
-
Hamalainen, H.K.1
Tubman, J.C.2
Vikman, S.3
Kyrola, T.4
Ylikoski, E.5
Warrington, J.A.6
Lahesmaa, R.7
-
22
-
-
0036363840
-
Introduction to microarray experimentation and analysis
-
S.W. Looney (ed.), Humana Press, Totowa, NJ
-
P. Gieser, G.C. Bloom, and E.N. Lazaridis. Introduction to microarray experimentation and analysis. In: Methods in Molecular Biology 184: Biostatistical Methods, S.W. Looney (ed.), pp. 29-49. Humana Press, Totowa, NJ, 2001.
-
(2001)
Methods in Molecular Biology 184: Biostatistical Methods
, pp. 29-49
-
-
Gieser, P.1
Bloom, G.C.2
Lazaridis, E.N.3
-
23
-
-
0037129827
-
Accurate normalization of real-time quantitative rt-pcr data by geometric averaging of multiple internal control genes
-
J. Vandesompele, K. De Preter, F. Pattyn, B. Poppe, N. Van Roy, A. De Paepe, and F. Speleman. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3: 0034.1-0034.11, 2002.
-
(2002)
Genome Biology
, vol.3
-
-
Vandesompele, J.1
De Preter, K.2
Pattyn, F.3
Poppe, B.4
Van Roy, N.5
De Paepe, A.6
Speleman, F.7
-
24
-
-
0041592552
-
Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction
-
X. Wang, M.J. Hessner, Y. Wu, N. Pati, and S. Ghosh. Quantitative quality control in microarray experiments and the application in data filtering, normalization and false positive rate prediction. Bioinformatics 19: 1341-1347, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 1341-1347
-
-
Wang, X.1
Hessner, M.J.2
Wu, Y.3
Pati, N.4
Ghosh, S.5
-
25
-
-
0035752668
-
Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data
-
E.E. Schadt, C. Li, B. Ellis, and W.H. Wong. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. Journal of Cellular Biochemistry 37 (Suppl): 120-125, 2001.
-
(2001)
Journal of Cellular Biochemistry
, vol.37
, pp. 120-125
-
-
Schadt, E.E.1
Li, C.2
Ellis, B.3
Wong, W.H.4
-
27
-
-
84947318637
-
Locally-weighted regression: An approach to regression analysis by local fitting
-
W.S. Cleveland and S.J. Devlin. Locally-weighted regression: an approach to regression analysis by local fitting. Journal of the American Statistical Association 83: 596-610, 1988.
-
(1988)
Journal of the American Statistical Association
, vol.83
, pp. 596-610
-
-
Cleveland, W.S.1
Devlin, S.J.2
-
28
-
-
4644304810
-
-
Insightful Corporation, Seattle, WA
-
Insightful. S+ArrayAnalyzer Version 1.1 software. Insightful Corporation, Seattle, WA, 2003.
-
(2003)
S+Arrayanalyzer Version 1.1 Software
-
-
-
29
-
-
0036376993
-
Statistical methods for identifying differentially expressed genes in replicated cdna microarray experiments
-
S. Dudoit, Y.H. Yang, M.J. Callow, and T.P. Speed. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica Sinica 12: 111-139, 2002.
-
(2002)
Statistica Sinica
, vol.12
, pp. 111-139
-
-
Dudoit, S.1
Yang, Y.H.2
Callow, M.J.3
Speed, T.P.4
-
30
-
-
0037225727
-
Contrast normalization of oligonucleotide arrays
-
M. Astrand. Contrast normalization of oligonucleotide arrays. Journal of Computational Biology 10: 95-102, 2003.
-
(2003)
Journal of Computational Biology
, vol.10
, pp. 95-102
-
-
Astrand, M.1
-
32
-
-
12344280017
-
Andt. P. Speed. Summaries of affymetrix genechip® probe level data
-
R.A. Irizarry, B.M. Bolstad, F. Collin, L.M. Cope, B. Hobbs, andT.P. Speed. Summaries of Affymetrix GeneChip® probe level data. Nucleic Acids Research 31: e15, 2003.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. e15
-
-
Irizarry, R.A.1
Bolstad, B.M.2
Collin, F.3
Cope, L.M.4
Hobbs, B.5
-
33
-
-
0142121516
-
Exploration, normalization, and summaries of high-density oligonucleotide array probe level data
-
R.A. Irizarry, B. Hobbs, F. Collin, Y.D. Beazer-Barclay, K.J. Antonellis, U. Scherf, and T.P. Speed. Exploration, normalization, and summaries of high-density oligonucleotide array probe level data. Biostatistics 4: 249-264, 2003.
-
(2003)
Biostatistics
, vol.4
, 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
-
-
0012397843
-
An r package for analysis of affymetrix oligonucleotide arrays
-
R.I.G. Parmigiani, E.S. Garrett, and S. Ziegler (eds.), Springer-Verlag, Berlin
-
R.A. Irizarry, L. Gautier, and L. Cope. An R package for analysis of Affymetrix oligonucleotide arrays. In: R.I.G. Parmigiani, E.S. Garrett, and S. Ziegler (eds.), The Analysis of Gene Expression Data: Methods and Software, pp. 102-119. Springer-Verlag, Berlin, 2003.
-
(2003)
The Analysis of Gene Expression Data: Methods and Software
, pp. 102-119
-
-
Irizarry, R.A.1
Gautier, L.2
Cope, L.3
-
35
-
-
0036126861
-
A systematic statistical linear modeling approach to oligonucleotide array experiments
-
T.M. Chu, B. Weir, and R.D. Wolfinger. A systematic statistical linear modeling approach to oligonucleotide array experiments. Mathematical Biosciences 176: 35-51, 2002.
-
(2002)
Mathematical Biosciences
, vol.176
, pp. 35-51
-
-
Chu, T.M.1
Weir, B.2
Wolfinger, R.D.3
-
36
-
-
1342294092
-
Normalization for cdna microarray data: A robust composite method addressing single and multiple slide systematic variation
-
Y.H. Yang, S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, and T.P. Speed. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Research 30: e15, 2002.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. e15
-
-
Yang, Y.H.1
Dudoit, S.2
Luu, P.3
Lin, D.M.4
Peng, V.5
Ngai, J.6
Speed, T.P.7
-
37
-
-
8144221593
-
Median-of-subsets normalization of intensities for cdna array data
-
R.R. Delongchamp, C. Velasco, M. Razzaghi, A. Harris, and D. Casciano. Median-of-subsets normalization of intensities for cDNA array data. DNA and Cell Biology23: 653-659, 2004.
-
(2004)
DNA and Cell Biology
, vol.23
, pp. 653-659
-
-
Delongchamp, R.R.1
Velasco, C.2
Razzaghi, M.3
Harris, A.4
Casciano, D.5
-
39
-
-
0036191188
-
Adjustments and measures of differential expression for microarray data
-
A. Tsodikov, A. Szabo, and D. Jones. Adjustments and measures of differential expression for microarray data. Bioinformatics 18: 251-260, 2002.
-
(2002)
Bioinformatics
, vol.18
, pp. 251-260
-
-
Tsodikov, A.1
Szabo, A.2
Jones, D.3
-
40
-
-
0037076772
-
Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis
-
R. Hoffmann, T. Seidl, and M. Dugas. Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biology 3: 0033.1-0033.11, 2002.
-
(2002)
Genome Biology
, vol.3
-
-
Hoffmann, R.1
Seidl, T.2
Dugas, M.3
-
41
-
-
0035749210
-
Evaluation of normalization procedures for oligonucleotide array data based on spiked crna controls
-
A.A. Hill, E.L. Brown, M.Z. Whitley, G. Tucker-Kellogg, C.P. Hunter, and D.K. Slonim. Evaluation of normalization procedures for oligonucleotide array data based on spiked cRNA controls. Genome Biology 2: 0055.1-0055.13, 2001.
-
(2001)
Genome Biology
, vol.2
-
-
Hill, A.A.1
Brown, E.L.2
Whitley, M.Z.3
Tucker-Kellogg, G.4
Hunter, C.P.5
Slonim, D.K.6
-
42
-
-
85057397223
-
Comparison of normalization methods and signal intensity measures for affymet-rix genechips®, marburg, germany
-
Berlin, November
-
O. Hartmann, B. Samans, D. Hoffman, J. WeBels, M. Klingenspor, and H. Schäfer. Comparison of normalization methods and signal intensity measures for Affymet-rix GeneChips®, Marburg, Germany. In: The Genetic and Molecular Basis of Human Disease. Proceedings of the Symposium of the German National Genome Research Network (NGFN) andthe GermanHuman Genome Project (DHGP), Berlin, November 2002.
-
(2002)
The Genetic and Molecular Basis of Human Disease
-
-
Hartmann, O.1
Samans, B.2
Hoffman, D.3
WeBels, J.4
Klingenspor, M.5
Schäfer, H.6
-
44
-
-
0034656561
-
Normalization strategies for cdna microarrays
-
J. Schuchhardt, D. Beule, A. Malik, E. Wolski, H. Eickhoff, H. Lehrach, and H. Herzel. Normalization strategies for cDNA microarrays. Nucleic Acids Research 28: e47, 2000.
-
(2000)
Nucleic Acids Research
, vol.28
, pp. e47
-
-
Schuchhardt, J.1
Beule, D.2
Malik, A.3
Wolski, E.4
Eickhoff, H.5
Lehrach, H.6
Herzel, H.7
-
45
-
-
0037188875
-
Normalization and analysis of dna microarray data by self-consistency and local regression
-
T.B. Kepler, L. Crosby, and K.T. Morgan. Normalization and analysis of DNA microarray data by self-consistency and local regression. Genome Biology 3: 0037.1-0037.12, 2002.
-
(2002)
Genome Biology
, vol.3
-
-
Kepler, T.B.1
Crosby, L.2
Morgan, K.T.3
-
46
-
-
0037200201
-
Knudsen. A new nonlinear normalization method for reducing variability in dna microarray experiments
-
C. Workman, L.J. Jensen, H. Jarmer, R. Berka, L. Gautier, H.B. Nielsen, H.H. Saxild, C. Nielsen, S. Brunak, and S. Knudsen. A new nonlinear normalization method for reducing variability in DNA microarray experiments. Genome Biology 3: 0048.1-0048.16, 2002.
-
(2002)
Genome Biology
, vol.3
-
-
Workman, C.1
Jensen, L.J.2
Jarmer, H.3
Berka, R.4
Gautier, L.5
Nielsen, H.B.6
Saxild, H.H.7
Nielsen, C.8
Brunak, S.9
-
47
-
-
0012572299
-
A variance-stabilizing transformation for gene-expression microarray data
-
B.P. Durbin, J.S. Hardin, D.M. Hawkins, and D.M. Rocke. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 18 (Suppl 1): S105-S110, 2002.
-
(2002)
Bioinformatics
, vol.18
, Issue.1
, pp. S105-S110
-
-
Durbin, B.P.1
Hardin, J.S.2
Hawkins, D.M.3
Rocke, D.M.4
-
48
-
-
0035987143
-
Local mean normalization of microarray element signal intensities across an array surface: Quality control and correction of spatially systematic artifacts
-
C. Colantuoni, G. Henry, S. Zeger, nad J. Pevsner. Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatially systematic artifacts. BioTechniques 32: 1316-1320, 2002.
-
(2002)
Biotechniques
, vol.32
, pp. 1316-1320
-
-
Colantuoni, C.1
Henry, G.2
Zeger, S.3
Pevsner, J.4
-
49
-
-
0036898577
-
Microarray data normalization and transformation
-
J. Quackenbush. Microarray data normalization and transformation. Nature Genetics32 (Suppl): 496-501, 2002.
-
(2002)
Nature Genetics
, vol.32
, pp. 496-501
-
-
Quackenbush, J.1
|