-
1
-
-
47949095131
-
A weighted average difference method for detecting differentially expressed genes from microarray data
-
10.1186/1748-7188-3-8
-
Kadota K Nakai Y Shimizu K A weighted average difference method for detecting differentially expressed genes from microarray data Algorithm Mol Biol 2008, 3:8. 10.1186/1748-7188-3-8
-
(2008)
Algorithm Mol Biol
, vol.3
, pp. 8
-
-
Kadota, K.1
Nakai, Y.2
Shimizu, K.3
-
2
-
-
42449144718
-
A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
-
2324099 18366762 10.1186/1471-2105-9-164
-
Pearson RD A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods BMC Bioinformatics 2008, 9:164. 2324099 18366762 10.1186/1471-2105-9-164
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 164
-
-
Pearson, R.D.1
-
3
-
-
33645326509
-
Comparison of Affymetrix GeneChip expression measures
-
10.1093/bioinformatics/btk046 16410320
-
Irizarry RA Wu Z Jaffee HA Comparison of Affymetrix GeneChip expression measures Bioinformatics 2006, 22(7):789-794. 10.1093/bioinformatics/ btk046 16410320
-
(2006)
Bioinformatics
, vol.22
, Issue.7
, pp. 789-794
-
-
Irizarry, R.A.1
Wu, Z.2
Jaffee, H.A.3
-
4
-
-
0036947892
-
Robust estimators for expression analysis
-
10.1093/bioinformatics/18.12.1585 12490442
-
Hubbell E Liu WM Mei R Robust estimators for expression analysis Bioinformatics 2002, 18:1585-1592. 10.1093/bioinformatics/18.12.1585 12490442
-
(2002)
Bioinformatics
, vol.18
, pp. 1585-1592
-
-
Hubbell, E.1
Liu, W.M.2
Mei, R.3
-
5
-
-
0142121516
-
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, 4:249-264. 10.1093/biostatistics/4.2.249 12925520
-
(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
-
6
-
-
33847288899
-
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
-
7
-
-
4344571581
-
Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
-
10.1016/j.febslet.2004.07.055 15327980
-
Breitling R Armengaud P Amtmann A Herzyk P Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments FEBS Lett 2004, 573(1-3):83-92. 10.1016/j.febslet.2004.07.055 15327980
-
(2004)
FEBS Lett
, vol.573
, Issue.1-3
, pp. 83-92
-
-
Breitling, R.1
Armengaud, P.2
Amtmann, A.3
Herzyk, P.4
-
8
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments
-
Article3 16646809
-
Smyth GK Linear models and empirical bayes methods for assessing differential expression in microarray experiments Stat Appl Genet Mol Biol 2004, 3:ARticle3 16646809
-
(2004)
Stat Appl Genet Mol Biol
, vol.3
-
-
Smyth, G.K.1
-
9
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
33173 11309499 10.1073/pnas.091062498
-
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. 33173 11309499 10.1073/pnas.091062498
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, Issue.9
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
10
-
-
33847302479
-
Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach
-
Article9 16646809
-
Opgen-Rhein R Strimmer K Accurate ranking of differentially expressed genes by a distribution-free shrinkage approach Stat Appl Genet Mol Biol 2007, 6:ARticle9 16646809
-
(2007)
Stat Appl Genet Mol Biol
, vol.6
-
-
Opgen-Rhein, R.1
Strimmer, K.2
-
11
-
-
33846786836
-
Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments
-
1781470 17177995 10.1186/1471-2105-7-538
-
Sartor MA Tomlinson CR Wesselkamper SC Sivaganesan S Leikauf GD Medvedovic M Intensity-based hierarchical Bayes method improves testing for differentially expressed genes in microarray experiments BMC Bioinformatics 2006, 7:538. 1781470 17177995 10.1186/1471-2105-7-538
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 538
-
-
Sartor, M.A.1
Tomlinson, C.R.2
Wesselkamper, S.C.3
Sivaganesan, S.4
Leikauf, G.D.5
Medvedovic, M.6
-
12
-
-
0035793042
-
Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
-
14539 11134512 10.1073/pnas.011404098
-
Li C Wong WH Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection Proc Natl Acad Sci USA 2001, 98:31-36. 14539 11134512 10.1073/pnas.011404098
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.H.2
-
13
-
-
22144461265
-
Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
-
551536 15693945 10.1186/gb-2005-6-2-r16
-
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. 551536 15693945 10.1186/ gb-2005-6-2-r16
-
(2005)
Genome Biol
, vol.6
, Issue.2
-
-
Choe, S.E.1
Boutros, M.2
Michelson, A.M.3
Church, G.M.4
Halfon, M.S.5
-
14
-
-
33747819335
-
-
Affymetrix, Santa Clala, California
-
Hubbel E PLIER White Paper Affymetrix, Santa Clala, California 2005
-
(2005)
PLIER White Paper
-
-
Hubbel, E.1
-
15
-
-
10844290766
-
A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
-
10.1198/016214504000000683
-
Wu Z Irizarry RA Gentleman R Martinez-Murillo F Spencer F A Model-Based Background Adjustment for Oligonucleotide Expression Arrays J Am Stat Assoc 2004, 99(468):909-918. 10.1198/016214504000000683
-
(2004)
J Am Stat Assoc
, vol.99
, Issue.468
, pp. 909-918
-
-
Wu, Z.1
Irizarry, R.A.2
Gentleman, R.3
Martinez-Murillo, F.4
Spencer, F.5
-
16
-
-
24644460573
-
A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips
-
10.1093/bioinformatics/bti583 16020470
-
Liu X Milo M Lawrence ND Rattray M A tractable probabilistic model for Affymetrix probe-level analysis across multiple chips Bioinformatics 2005, 21(18):3637-3644. 10.1093/bioinformatics/bti583 16020470
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3637-3644
-
-
Liu, X.1
Milo, M.2
Lawrence, N.D.3
Rattray, M.4
-
17
-
-
33645823677
-
A new summarization method for Affymetrix probe level data
-
10.1093/bioinformatics/btl033 16473874
-
Hochreiter S Clevert DA Obermayer K A new summarization method for Affymetrix probe level data Bioinformatics 2006, 22(8):943-949. 10.1093/ bioinformatics/btl033 16473874
-
(2006)
Bioinformatics
, vol.22
, Issue.8
, pp. 943-949
-
-
Hochreiter, S.1
Clevert, D.A.2
Obermayer, K.3
-
18
-
-
0034948896
-
A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inference of gene changes
-
10.1093/bioinformatics/17.6.509 11395427
-
Baldi P Long AD A Bayesian framework for the analysis of microarray expression data: Regularized t-test and statistical inference of gene changes Bioinformatics 2001, 17:509-519. 10.1093/bioinformatics/17.6.509 11395427
-
(2001)
Bioinformatics
, vol.17
, pp. 509-519
-
-
Baldi, P.1
Long, A.D.2
-
19
-
-
33748644662
-
Probe-level measurement error improves accuracy in detecting differential gene expression
-
10.1093/bioinformatics/btl361 16820429
-
Liu X Milo M Lawrence ND Rattray M Probe-level measurement error improves accuracy in detecting differential gene expression Bioinformatics 2006, 22(17):2107-2113. 10.1093/bioinformatics/btl361 16820429
-
(2006)
Bioinformatics
, vol.22
, Issue.17
, pp. 2107-2113
-
-
Liu, X.1
Milo, M.2
Lawrence, N.D.3
Rattray, M.4
-
20
-
-
11244346557
-
Variance stabilization applied to microarray data calibration and to the quantification of differential expression
-
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. 12169536
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Huber, W.1
von Heydebreck, A.2
Sultmann, H.3
Poustka, A.4
Vingron, M.5
-
21
-
-
33748491517
-
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
-
MAQC Consortium 10.1038/nbt1239 16964229
-
MAQC Consortium The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat Biotechnol 2006, 24(9):1151-1161. 10.1038/nbt1239 16964229
-
(2006)
Nat Biotechnol
, vol.24
, Issue.9
, pp. 1151-1161
-
-
-
23
-
-
65549127050
-
-
AffyDEComp website http://www.bioinf.manchester.ac.uk/affydecomp/
-
AffyDEComp Website
-
-
-
24
-
-
34447333663
-
GOGOT: A method for the identification of differentially expressed fragments from cDNA-AFLP data
-
10.1186/1748-7188-2-5
-
Kadota K Araki R Nakai Y Abe M GOGOT: A method for the identification of differentially expressed fragments from cDNA-AFLP data Algorithm Mol Biol 2007, 2:5. 10.1186/1748-7188-2-5
-
(2007)
Algorithm Mol Biol
, vol.2
, pp. 5
-
-
Kadota, K.1
Araki, R.2
Nakai, Y.3
Abe, M.4
-
25
-
-
49649083648
-
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
-
2537561 18793455 10.1186/1471-2105-9-S9-S10
-
Shi L Jones WD Jensen RV Harris SC Perkins RG Goodsaid FM Guo L Croner LJ Boysen C Fang H Qian F Amur S Bao W Barbacioru CC Bertholet V Cao XM Chu TM Collins PJ Fan XH Frueh FW Fuscoe JC Guo X Han J Herman D Hong H Kawasaki ES Li QZ Luo Y Ma Y Mei N Peterson RL Puri RK Shippy R Su Z Sun YA Sun H Thorn B Turpaz Y Wang C Wang SJ Warrington JA Willey JC Wu J Xie Q Zhang L Zhang L Zhong S Wolfinger RD Tong W The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies BMC Bioinformatics 2008, 9(Suppl 9):S10. 2537561 18793455 10.1186/1471-2105-9-S9-S10
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 9
-
-
Shi, L.1
Jones, W.D.2
Jensen, R.V.3
Harris, S.C.4
Perkins, R.G.5
Goodsaid, F.M.6
Guo, L.7
Croner, L.J.8
Boysen, C.9
Fang, H.10
Qian, F.11
Amur, S.12
Bao, W.13
Barbacioru, C.C.14
Bertholet, V.15
Cao, X.M.16
Chu, T.M.17
Collins, P.J.18
Fan, X.H.19
Frueh, F.W.20
Fuscoe, J.C.21
Guo, X.22
Han, J.23
Herman, D.24
Hong, H.25
Kawasaki, E.S.26
Li, Q.Z.27
Luo, Y.28
Ma, Y.29
Mei, N.30
Peterson, R.L.31
Puri, R.K.32
Shippy, R.33
Su, Z.34
Sun, Y.A.35
Sun, H.36
Thorn, B.37
Turpaz, Y.38
Wang, C.39
Wang, S.J.40
Warrington, J.A.41
Willey, J.C.42
Wu, J.43
Xie, Q.44
Zhang, L.45
Zhang, L.46
Zhong, S.47
Wolfinger, R.D.48
Tong, W.49
more..
-
26
-
-
33749326335
-
Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression
-
1579233 16934150 10.1186/1471-2105-7-391
-
Lemieux S Probe-level linear model fitting and mixture modeling results in high accuracy detection of differential gene expression BMC Bioinformatics 2006, 7:391. 1579233 16934150 10.1186/1471-2105-7-391
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 391
-
-
Lemieux, S.1
-
27
-
-
41949124937
-
Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays
-
10.1093/bioinformatics/btn053 18316342
-
Xu J Cui X Robustified MANOVA with applications in detecting differentially expressed genes from oligonucleotide arrays Bioinformatics 2008, 24(8):1056-1062. 10.1093/bioinformatics/btn053 18316342
-
(2008)
Bioinformatics
, vol.24
, Issue.8
, pp. 1056-1062
-
-
Xu, J.1
Cui, X.2
-
28
-
-
38549112328
-
Up-regulation of genes related to the ubiquitin-proteasome system in the brown adipose tissue of 24-h-fasted rats
-
10.1271/bbb.70508 18175912
-
Nakai Y Hashida H Kadota K Minami M Shimizu K Matsumoto I Kato H Abe K Up-regulation of genes related to the ubiquitin-proteasome system in the brown adipose tissue of 24-h-fasted rats Biosci Biotechnol Biochem 2008, 72(1):139-148. 10.1271/bbb.70508 18175912
-
(2008)
Biosci Biotechnol Biochem
, vol.72
, Issue.1
, pp. 139-148
-
-
Nakai, Y.1
Hashida, H.2
Kadota, K.3
Minami, M.4
Shimizu, K.5
Matsumoto, I.6
Kato, H.7
Abe, K.8
-
29
-
-
42549092565
-
A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays
-
2375129 18410691 10.1186/1471-2105-9-194
-
Ge H Cheng C Li LM A probe-treatment-reference (PTR) model for the analysis of oligonucleotide expression microarrays BMC Bioinformatics 2008, 9:194. 2375129 18410691 10.1186/1471-2105-9-194
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 194
-
-
Ge, H.1
Cheng, C.2
Li, L.M.3
-
30
-
-
52649112095
-
"Hook"-calibration of GeneChip-microarrays: Theory and algorithm
-
10.1186/1748-7188-3-12
-
Binder H Preibisch S "Hook"-calibration of GeneChip-microarrays: Theory and algorithm Algorithm Mol Biol 2008, 3:12. 10.1186/1748-7188-3-12
-
(2008)
Algorithm Mol Biol
, vol.3
, pp. 12
-
-
Binder, H.1
Preibisch, S.2
-
31
-
-
52649161839
-
"Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures
-
10.1186/1748-7188-3-11
-
Binder H Krohn K Preibisch S "Hook"-calibration of GeneChip-microarrays: Chip characteristics and expression measures Algorithm Mol Biol 2008, 3:11. 10.1186/1748-7188-3-11
-
(2008)
Algorithm Mol Biol
, vol.3
, pp. 11
-
-
Binder, H.1
Krohn, K.2
Preibisch, S.3
-
32
-
-
33846064113
-
NCBI GEO: Mining tens of millions of expression profiles-database and tools update
-
1669752 17099226 10.1093/nar/gkl887
-
Barrett T Troup DB Wilhite SE Ledoux P Rudnev D Evangelista C Kim IF Soboleva A Tomashevsky M Edgar R NCBI GEO: Mining tens of millions of expression profiles-database and tools update Nucleic Acids Res 2007, 35:D760-D765. 1669752 17099226 10.1093/nar/gkl887
-
(2007)
Nucleic Acids Res
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Rudnev, D.5
Evangelista, C.6
Kim, I.F.7
Soboleva, A.8
Tomashevsky, M.9
Edgar, R.10
-
34
-
-
28744458859
-
Bioconductor: Open software development for computational biology and bioinformatics
-
545600 15461798 10.1186/gb-2004-5-10-r80
-
Gentleman RC Carey VJ Bates DM Bolstad B Dettling M Dudoit S Ellis B Gautier L Ge Y Gentry J Hornik K Hothorn T Huber W Iacus S Irizarry R Leisch F Li C Maechler M Rossini AJ Sawitzki G Smith C Smyth G Tierney L Yang JY Zhang J Bioconductor: Open software development for computational biology and bioinformatics Genome Biol 2004, 5(10):R80. 545600 15461798 10.1186/gb-2004-5-10-r80
-
(2004)
Genome Biol
, vol.5
, Issue.10
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
Ellis, B.7
Gautier, L.8
Ge, Y.9
Gentry, J.10
Hornik, K.11
Hothorn, T.12
Huber, W.13
Iacus, S.14
Irizarry, R.15
Leisch, F.16
Li, C.17
Maechler, M.18
Rossini, A.J.19
Sawitzki, G.20
Smith, C.21
Smyth, G.22
Tierney, L.23
Yang, J.Y.24
Zhang, J.25
more..
-
35
-
-
1342288026
-
Affy-analysis of Affymetrix GeneChip data at probe level
-
10.1093/bioinformatics/btg405 14960456
-
Gautier L Cope L Bolstad BM Irizarry RA affy-analysis of Affymetrix GeneChip data at probe level Bioinformatics 2004, 20(3):307-315. 10.1093/ bioinformatics/btg405 14960456
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 307-315
-
-
Gautier, L.1
Cope, L.2
Bolstad, B.M.3
Irizarry, R.A.4
-
36
-
-
33751006151
-
RankProd: A Bioconductor package for detecting differentially expressed genes in meta-analysis
-
10.1093/bioinformatics/btl476 16982708
-
Hong F Breitling R McEntee CW Wittner BS Nemhauser JL Chory J RankProd: a Bioconductor package for detecting differentially expressed genes in meta-analysis Bioinformatics 2006, 22(22):2825-2827. 10.1093/ bioinformatics/btl476 16982708
-
(2006)
Bioinformatics
, vol.22
, Issue.22
, pp. 2825-2827
-
-
Hong, F.1
Breitling, R.2
McEntee, C.W.3
Wittner, B.S.4
Nemhauser, J.L.5
Chory, J.6
-
37
-
-
65549100860
-
-
The R-code for DFW http://faculty.smu.edu/mmcgee/dfwcode.pdf
-
The R-code for DFW
-
-
-
39
-
-
84888285061
-
-
The MAQC website http://edkb.fda.gov/MAQC/MainStudy/upload/
-
The MAQC Website
-
-
|