-
1
-
-
27544492493
-
Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data
-
Xu L, Tan AC, Naiman DQ, Geman D, Winslow RL. Robust prostate cancer marker genes emerge from direct integration of inter-study microarray data. Bioinfometics 2005; 21(20):3905-3911.
-
(2005)
Bioinfometics
, vol.21
, Issue.20
, pp. 3905-3911
-
-
Xu, L.1
Tan, A.C.2
Naiman, D.Q.3
Geman, D.4
Winslow, R.L.5
-
2
-
-
13444249852
-
Prediction of cancer outcome with microarrays: a multiple random validation strategy
-
Michiels S, Koscielny S, Hill C. Prediction of cancer outcome with microarrays: a multiple random validation strategy. Lancet 2005; 365(9458):488-492.
-
(2005)
Lancet
, vol.365
, Issue.9458
, pp. 488-492
-
-
Michiels, S.1
Koscielny, S.2
Hill, C.3
-
4
-
-
67649197934
-
Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction
-
Cheng C, Shen K, Song C, Luo J, Tseng GC. Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction. Bioinformatics 2009; 25(13):1655-1661.
-
(2009)
Bioinformatics
, vol.25
, Issue.13
, pp. 1655-1661
-
-
Cheng, C.1
Shen, K.2
Song, C.3
Luo, J.4
Tseng, G.C.5
-
6
-
-
1842559788
-
Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments
-
Baggerly KA, Morris JS, Coombes KR. Reproducibility of SELDI-TOF protein patterns in serum: comparing datasets from different experiments. Bioinformatics 2004; 20: 777-785.
-
(2004)
Bioinformatics
, vol.20
, pp. 777-785
-
-
Baggerly, K.A.1
Morris, J.S.2
Coombes, K.R.3
-
7
-
-
19944429996
-
Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays
-
Dobbin KK, Beer DG, Meyerson M, Yeatman TJ, Gerald WL, Jacobson JW, Conley B, Buetow KH, Heiskanen M, Simon RM, Minna JD, Girard L, Misek DE, Taylor JMG, Hanash S, Naoki K, Hayes DN, Ladd-Acosta C, Enkemann SA, Viale A, Giordano TJ. Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clinical Cancer Research 2005; 11: 565-572.
-
(2005)
Clinical Cancer Research
, vol.11
, pp. 565-572
-
-
Dobbin, K.K.1
Beer, D.G.2
Meyerson, M.3
Yeatman, T.J.4
Gerald, W.L.5
Jacobson, J.W.6
Conley, B.7
Buetow, K.H.8
Heiskanen, M.9
Simon, R.M.10
Minna, J.D.11
Girard, L.12
Misek, D.E.13
Taylor, J.M.G.14
Hanash, S.15
Naoki, K.16
Hayes, D.N.17
Ladd-Acosta, C.18
Enkemann, S.A.19
Viale, A.20
Giordano, T.J.21
more..
-
8
-
-
18244384210
-
Multiple-laboratory comparison of microarray platforms
-
Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Gabrielson BC, Frank E, Garcia JGN, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martinez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W. Multiple-laboratory comparison of microarray platforms. Nature Methods 2005; 2(5):345-350.
-
(2005)
Nature Methods
, vol.2
, Issue.5
, pp. 345-350
-
-
Irizarry, R.A.1
Warren, D.2
Spencer, F.3
Kim, I.F.4
Biswal, S.5
Gabrielson, B.C.6
Frank, E.7
Garcia, J.G.N.8
Geoghegan, J.9
Germino, G.10
Griffin, C.11
Hilmer, S.C.12
Hoffman, E.13
Jedlicka, A.E.14
Kawasaki, E.15
Martinez-Murillo, F.16
Morsberger, L.17
Lee, H.18
Petersen, D.19
Quackenbush, J.20
Scott, A.21
Wilson, M.22
Yang, Y.23
Ye, S.Q.24
Yu, W.25
more..
-
9
-
-
33748491517
-
The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
MAQC Consortium.
-
MAQC Consortium. The microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nature Biotechnology 2006; 24: 1151-1161.
-
(2006)
Nature Biotechnology
, vol.24
, pp. 1151-1161
-
-
-
11
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews Genetics 2010; 11: 733-739.
-
(2010)
Nature Reviews Genetics
, vol.11
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
Johnson, W.E.6
Geman, D.7
Baggerly, K.8
Irizarry, R.A.9
-
12
-
-
49149129916
-
Gene-expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study
-
Shedden K, Taylor JMG, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Venkatraman SE, Meyerson M, Kuick R, Dobbin KK, Lively T, Jacobson JW, Beer DG, Giordano TJ, Misek DE, Chang AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Szoke J, Zakowski M, Rusch V, Kris M, Viale A, Motoi N, Travis W, Sharma A. Gene-expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nature Medicine 2008; 14(8):822-827.
-
(2008)
Nature Medicine
, vol.14
, Issue.8
, pp. 822-827
-
-
Shedden, K.1
Taylor, J.M.G.2
Enkemann, S.A.3
Tsao, M.S.4
Yeatman, T.J.5
Gerald, W.L.6
Eschrich, S.7
Jurisica, I.8
Venkatraman, S.E.9
Meyerson, M.10
Kuick, R.11
Dobbin, K.K.12
Lively, T.13
Jacobson, J.W.14
Beer, D.G.15
Giordano, T.J.16
Misek, D.E.17
Chang, A.C.18
Zhu, C.Q.19
Strumpf, D.20
Hanash, S.21
Shepherd, F.A.22
Ding, K.23
Seymour, L.24
Naoki, K.25
Pennell, N.26
Weir, B.27
Verhaak, R.28
Ladd-Acosta, C.29
Golub, T.30
Gruidl, M.31
Szoke, J.32
Zakowski, M.33
Rusch, V.34
Kris, M.35
Viale, A.36
Motoi, N.37
Travis, W.38
Sharma, A.39
more..
-
14
-
-
0347090327
-
Adjustment of systematic microarray data biases
-
Benito M, Parker J, Du Q, Wu J, Xiang D, Perou CM, Marron JS. Adjustment of systematic microarray data biases. Bioinformatics 2004; 20(1):105-114.
-
(2004)
Bioinformatics
, vol.20
, Issue.1
, pp. 105-114
-
-
Benito, M.1
Parker, J.2
Du, Q.3
Wu, J.4
Xiang, D.5
Perou, C.M.6
Marron, J.S.7
-
15
-
-
33845432928
-
Adjusting batch effects in microarray expression data using empirical Bayes methods
-
Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007; 8(1):118-127.
-
(2007)
Biostatistics
, vol.8
, Issue.1
, pp. 118-127
-
-
Johnson, W.E.1
Li, C.2
Rabinovic, A.3
-
16
-
-
34848914038
-
Capturing heterogeneity in gene expression studies by surrogate variable analysis
-
Leek JT, Storey JD. Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics 2007; 3(9):e161.
-
(2007)
PLoS Genetics
, vol.3
, Issue.9
-
-
Leek, J.T.1
Storey, J.D.2
-
17
-
-
42649134796
-
Merging two gene-expression studies via cross-platform normalization
-
Shabalin AA, Tjelmeland H, Fan C, Perou CM, Nobel AB. Merging two gene-expression studies via cross-platform normalization. Bioinformatics 2008; 24(9):1154-1160.
-
(2008)
Bioinformatics
, vol.24
, Issue.9
, pp. 1154-1160
-
-
Shabalin, A.A.1
Tjelmeland, H.2
Fan, C.3
Perou, C.M.4
Nobel, A.B.5
-
18
-
-
84862250978
-
Using control genes to correct for unwanted variation in microarray data
-
Gagnon-Bartsch JA, Speed TP. Using control genes to correct for unwanted variation in microarray data. Biostatistics 2012; 13(3):539-552.
-
(2012)
Biostatistics
, vol.13
, Issue.3
, pp. 539-552
-
-
Gagnon-Bartsch, J.A.1
Speed, T.P.2
-
19
-
-
55349144848
-
High dimensional covariance matrix estimation using a factor model
-
Fan J, Fan Y, Lv J. High dimensional covariance matrix estimation using a factor model. Journal of Econometrics 2008; 147: 186-197.
-
(2008)
Journal of Econometrics
, vol.147
, pp. 186-197
-
-
Fan, J.1
Fan, Y.2
Lv, J.3
-
20
-
-
62549125109
-
High-dimensional sparse factor modeling: applications in gene expression genomics
-
Carvalho CM, Chang J, Lucas JE, Nevins JR, Wang Q, West M. High-dimensional sparse factor modeling: applications in gene expression genomics. Journal of the American Statistical Association 2008; 103(484):1438-1456.
-
(2008)
Journal of the American Statistical Association
, vol.103
, Issue.484
, pp. 1438-1456
-
-
Carvalho, C.M.1
Chang, J.2
Lucas, J.E.3
Nevins, J.R.4
Wang, Q.5
West, M.6
-
22
-
-
65549126939
-
Gene set internal coherence in the context of functional profiling
-
DOI: 10.1186/1471-2164-10-197.
-
Montaner D, Minguez P, Al-Shahrour F, Dopazo J. Gene set internal coherence in the context of functional profiling. BMC Genomics 2009; 10: 1-13. DOI: 10.1186/1471-2164-10-197.
-
(2009)
BMC Genomics
, vol.10
, pp. 1-13
-
-
Montaner, D.1
Minguez, P.2
Al-Shahrour, F.3
Dopazo, J.4
-
23
-
-
69249109724
-
Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine
-
DOI: 10.1371/journal.pone.0006669.
-
Claesson MJ, O'Sullivan O, Wang Q, Nikkila J, Marchesi JR, Smidt H, deVos WM, Ross RP, O'Toole PW. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PLoS ONE 2009; 4: 1-15. DOI: 10.1371/journal.pone.0006669.
-
(2009)
PLoS ONE
, vol.4
, pp. 1-15
-
-
Claesson, M.J.1
O'Sullivan, O.2
Wang, Q.3
Nikkila, J.4
Marchesi, J.R.5
Smidt, H.6
deVos, W.M.7
Ross, R.P.8
O'Toole, P.W.9
-
24
-
-
62349112885
-
Covariance regularization by thresholding
-
Bickel PJ, Levina E. Covariance regularization by thresholding. The Annals of Statistics 2008; 36(6):2577-2604.
-
(2008)
The Annals of Statistics
, vol.36
, Issue.6
, pp. 2577-2604
-
-
Bickel, P.J.1
Levina, E.2
-
25
-
-
79960133776
-
Adaptive thresholding for sparse covariance matrix estimation
-
Cai T, Liu W. Adaptive thresholding for sparse covariance matrix estimation. Journal of the American Statistical Association 2011; 106(494):672-684.
-
(2011)
Journal of the American Statistical Association
, vol.106
, Issue.494
, pp. 672-684
-
-
Cai, T.1
Liu, W.2
-
26
-
-
77949541881
-
Testing the equality of several covariance matrices with fewer observations than the dimension
-
Srivastava MS, Yanagihara H. Testing the equality of several covariance matrices with fewer observations than the dimension. Journal of Multivariate Analysis 2010; 101: 1319-1329.
-
(2010)
Journal of Multivariate Analysis
, vol.101
, pp. 1319-1329
-
-
Srivastava, M.S.1
Yanagihara, H.2
-
27
-
-
80052664177
-
Regularized discriminant analysis and its application in microarrays
-
Guo Y, Hastie T, Tibshirani R. Regularized discriminant analysis and its application in microarrays. Biostatistics 2005; 1(1):1-18.
-
(2005)
Biostatistics
, vol.1
, Issue.1
, pp. 1-18
-
-
Guo, Y.1
Hastie, T.2
Tibshirani, R.3
-
28
-
-
77955131271
-
A comparison of batch effect removal methods for enhancement of prediction performance using MARQ-II microarray gene expression data
-
Luo J, Schumacher M, Scherer A, Sanoudou D, Megherbi D, Davison T, Shi T, Tong W, Shi L, Hong H, Zhao C, Elloumi F, Shi W, Thomas R, Lin S, Tillinghast G, Liu G, Zhou Y, Herman D, Li Y, Deng Y, Fang H, Bushel P, Woods M, Zhang J. A comparison of batch effect removal methods for enhancement of prediction performance using MARQ-II microarray gene expression data. The Pharmacogenomics Journal 2010; 10: 278-291.
-
(2010)
The Pharmacogenomics Journal
, vol.10
, pp. 278-291
-
-
Luo, J.1
Schumacher, M.2
Scherer, A.3
Sanoudou, D.4
Megherbi, D.5
Davison, T.6
Shi, T.7
Tong, W.8
Shi, L.9
Hong, H.10
Zhao, C.11
Elloumi, F.12
Shi, W.13
Thomas, R.14
Lin, S.15
Tillinghast, G.16
Liu, G.17
Zhou, Y.18
Herman, D.19
Li, Y.20
Deng, Y.21
Fang, H.22
Bushel, P.23
Woods, M.24
Zhang, J.25
more..
-
30
-
-
70449588688
-
Can survival prediction be improved by merging gene expression data sets?
-
Yasrebi H, Sperisen P, Praz V, Bucher P. Can survival prediction be improved by merging gene expression data sets?. PLoS ONE 2009; 4(10):e7431.
-
(2009)
PLoS ONE
, vol.4
, Issue.10
-
-
Yasrebi, H.1
Sperisen, P.2
Praz, V.3
Bucher, P.4
-
31
-
-
15944419638
-
Efficient quadratic regularization for expression arrays
-
Hastie T, Tibshirani R. Efficient quadratic regularization for expression arrays. Biostatistics 2004; 5(3):329-340.
-
(2004)
Biostatistics
, vol.5
, Issue.3
, pp. 329-340
-
-
Hastie, T.1
Tibshirani, R.2
|