-
1
-
-
0036898577
-
Microarray data normalisation and transformation
-
12454644 10.1038/ng1032
-
Quackenbush J Microarray data normalisation and transformation Nature Genetics 2002 32 496-501 12454644 10.1038/ng1032
-
(2002)
Nature Genetics
, vol.32
, pp. 496-501
-
-
Quackenbush, J.1
-
2
-
-
33645326509
-
Comparison of Affymetrix GeneChip expression measures
-
16410320 10.1093/bioinformatics/btk046
-
Irizarry R Wu Z Jaffee H Comparison of Affymetrix GeneChip expression measures Bioinformatics 2006 22 789 16410320 10.1093/bioinformatics/ btk046
-
(2006)
Bioinformatics
, vol.22
, pp. 789
-
-
Irizarry, R.1
Wu, Z.2
Jaffee, H.3
-
3
-
-
2342439256
-
Comparative analysis of algorithms for signal quantification from oligonucleotide microarrays
-
10.1093/bioinformatics/btg487 14751998
-
Barash Y Dehan E Krupsky M Franklin W Geraci M Friedman N Kamiski N Comparative analysis of algorithms for signal quantification from oligonucleotide microarrays Bioinformatics 2004 20 6 839-846 10.1093/ bioinformatics/btg487 14751998
-
(2004)
Bioinformatics
, vol.20
, Issue.6
, pp. 839-846
-
-
Barash, Y.1
Dehan, E.2
Krupsky, M.3
Franklin, W.4
Geraci, M.5
Friedman, N.6
Kamiski, N.7
-
4
-
-
33748809521
-
Probe set algorithms: Is there a rational best bet?
-
1569879 16942624 10.1186/1471-2105-7-395
-
Seo J Hoffman E Probe set algorithms: Is there a rational best bet? BMC Bioinformatics 2006 7 395 1569879 16942624 10.1186/1471-2105-7-395
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 395
-
-
Seo, J.1
Hoffman, E.2
-
5
-
-
0037076772
-
Profound effects of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis
-
research0033 126238 12184807 10.1186/gb-2002-3-7-research0033
-
Hoffmann R Seidl T Dugas M Profound effects of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis Genome Biology 2002 3 7 research0033 126238 12184807 10.1186/gb-2002-3-7-research0033
-
(2002)
Genome Biology
, vol.3
, Issue.7
-
-
Hoffmann, R.1
Seidl, T.2
Dugas, M.3
-
6
-
-
29144535372
-
"Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data"
-
1283542 16284200 10.1093/nar/gni179
-
Dai M Wang P Boyd A Kostov G Athey B Jones E Bunney W Myers R Speed T Akil H Watson S Meng F "Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data" Nucleic Acids Research 2005 33 20 e175 1283542 16284200 10.1093/nar/gni179
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.20
-
-
Dai, M.1
Wang, P.2
Boyd, A.3
Kostov, G.4
Athey, B.5
Jones, E.6
Bunney, W.7
Myers, R.8
Speed, T.9
Akil, H.10
Watson, S.11
Meng, F.12
-
7
-
-
34347396264
-
"Comparisons of annotation predictions for Affymetrix GeneChips"
-
10.2165/00822942-200605040-00006 17140270
-
Stalteri M Harrison A "Comparisons of annotation predictions for Affymetrix GeneChips" Applied Bioinformatics 2006 5 4 237 10.2165/ 00822942-200605040-00006 17140270
-
(2006)
Applied Bioinformatics
, vol.5
, Issue.4
, pp. 237
-
-
Stalteri, M.1
Harrison, A.2
-
8
-
-
33846986793
-
"Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips"
-
1784106 17224057 10.1186/1471-2105-8-13
-
Stalteri M Harrison A "Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips" BMC Bioinformatics 2007 8 13 1784106 17224057 10.1186/1471-2105-8-13
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 13
-
-
Stalteri, M.1
Harrison, A.2
-
9
-
-
0037069368
-
"Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) from normal skeletal muscle"
-
137534 12415109 10.1073/pnas.192571199
-
Haslett J Sanoudou D Kho A Bennett R Greenberg S Kohane I Beggs A Kunkel L "Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) from normal skeletal muscle" PNAS 2002 99 15000 137534 12415109 10.1073/pnas.192571199
-
(2002)
PNAS
, vol.99
, pp. 15000
-
-
Haslett, J.1
Sanoudou, D.2
Kho, A.3
Bennett, R.4
Greenberg, S.5
Kohane, I.6
Beggs, A.7
Kunkel, L.8
-
10
-
-
0142121516
-
"Exploration, normalization and summaries of high density oligonucleotide array probe level data"
-
10.1093/biostatistics/4.2.249 12925520
-
Irizarry R Hobbs B Collin F Beazer-Barclay Y Antonellis K Scherf U Speed T "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.1
Hobbs, B.2
Collin, F.3
Beazer-Barclay, Y.4
Antonellis, K.5
Scherf, U.6
Speed, T.7
-
12
-
-
0035793042
-
"Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection"
-
14539 11134512 10.1073/pnas.011404098
-
Li C Wong W "Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection" PNAS 2001 98 31-36 14539 11134512 10.1073/pnas.011404098
-
(2001)
PNAS
, vol.98
, pp. 31-36
-
-
Li, C.1
Wong, W.2
-
13
-
-
6944256813
-
"Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise"
-
10.1038/ng1429 15448691
-
Mendell J Sharifi N Meyers J Martinez-Murillo F Dietz H "Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise" Nature Genetics 2004 36 1073 10.1038/ng1429 15448691
-
(2004)
Nature Genetics
, vol.36
, pp. 1073
-
-
Mendell, J.1
Sharifi, N.2
Meyers, J.3
Martinez-Murillo, F.4
Dietz, H.5
-
14
-
-
27544469776
-
"Chronic intermittent hypoxia upregualtes genes of lipid biosynthesis in obese mice"
-
10.1152/japplphysiol.00522.2005 16037401
-
Li J Grigoryev D Ye S-Q Thorne L Schwartz A Smith P O'Donnell C Polotsky V "Chronic intermittent hypoxia upregualtes genes of lipid biosynthesis in obese mice" Journal of Applied Physiology 2005 99 1643 10.1152/japplphysiol.00522.2005 16037401
-
(2005)
Journal of Applied Physiology
, vol.99
, pp. 1643
-
-
Li, J.1
Grigoryev, D.2
Ye, S.-Q.3
Thorne, L.4
Schwartz, A.5
Smith, P.6
O'Donnell, C.7
Polotsky, V.8
-
15
-
-
33645791665
-
"A physiogenomic approach to study the regulation of blood pressure"
-
10.1152/physiolgenomics.00077.2005 15942020
-
Westhoff T Scheid S Tölle M Kaynak B Schmidt S Zidek W Sperling S van der Giet M "A physiogenomic approach to study the regulation of blood pressure" Physiol Genomics 2005 23 46 10.1152/ physiolgenomics.00077.2005 15942020
-
(2005)
Physiol Genomics
, vol.23
, pp. 46
-
-
Westhoff, T.1
Scheid, S.2
Tölle, M.3
Kaynak, B.4
Schmidt, S.5
Zidek, W.6
Sperling, S.7
van der Giet, M.8
-
16
-
-
20944438747
-
"In chronic myeloid leukaemia white cells from cytogenetic responders and non-responders to imatinib have very similar gene expression signatures"
-
15820940
-
Crossman L Mori M Hsieh Y Lange T Paschka P Harrington C Krohn K Niederwieser D Hehlmann R Hochhaus A Druker B Deininger M "In chronic myeloid leukaemia white cells from cytogenetic responders and non-responders to imatinib have very similar gene expression signatures" Haematologica 2005 90 4 459 15820940
-
(2005)
Haematologica
, vol.90
, Issue.4
, pp. 459
-
-
Crossman, L.1
Mori, M.2
Hsieh, Y.3
Lange, T.4
Paschka, P.5
Harrington, C.6
Krohn, K.7
Niederwieser, D.8
Hehlmann, R.9
Hochhaus, A.10
Druker, B.11
Deininger, M.12
-
17
-
-
85035214096
-
"Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays"
-
011906
-
Naef F Magnasco M "Solving the riddle of the bright mismatches: Labeling and effective binding in oligonucleotide arrays" Physical Review (E) 2003 68 1 Pt 1 011906
-
(2003)
Physical Review (E)
, vol.68
, Issue.1 PART 1
-
-
Naef, F.1
Magnasco, M.2
-
18
-
-
0038729666
-
"A model of molecular interactions on short oligonucleotide microarrays"
-
10.1038/nbt836 12794640
-
Zhang L Miles M Aldape K "A model of molecular interactions on short oligonucleotide microarrays" Nature Biotechnology 2003 21 7 818 10.1038/nbt836 12794640
-
(2003)
Nature Biotechnology
, vol.21
, Issue.7
, pp. 818
-
-
Zhang, L.1
Miles, M.2
Aldape, K.3
-
19
-
-
0037388263
-
"Absolute mRNA concentrations from sequence specific calibration of oligonucleotide arrays"
-
152799 12655013 10.1093/nar/gkg283
-
Hekstra D Taussig A Magnasco M Naef F "Absolute mRNA concentrations from sequence specific calibration of oligonucleotide arrays" Nucleic Acids Research 2003 31 7 1962-1968 152799 12655013 10.1093/nar/ gkg283
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.7
, pp. 1962-1968
-
-
Hekstra, D.1
Taussig, A.2
Magnasco, M.3
Naef, F.4
-
20
-
-
25444494145
-
"Correlation test to assess low-level processing of high-density oligonucleotide microarray data"
-
1084343 15799785 10.1186/1471-2105-6-80
-
Ploner A Miller L Hall P Bergh J Pawitan Y "Correlation test to assess low-level processing of high-density oligonucleotide microarray data" BMC Bioinformatics 2005 6 80 1084343 15799785 10.1186/ 1471-2105-6-80
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 80
-
-
Ploner, A.1
Miller, L.2
Hall, P.3
Bergh, J.4
Pawitan, Y.5
-
22
-
-
34347402919
-
Reply to the letter of Klebanov et al
-
MACQ consortium 10.1038/nbt0107-26
-
Shi L MACQ consortium Reply to the letter of Klebanov et al Nature Biotechnology 2007 25 26 10.1038/nbt0107-26
-
(2007)
Nature Biotechnology
, vol.25
, pp. 26
-
-
Shi, L.1
-
23
-
-
33748495591
-
"Rat toxicogenomic study reveals analytical consistency across microarray platforms"
-
10.1038/nbt1238 17061323
-
Guo L Lobenhofer E Wang C Shippy R Harris S Zhang L Mei N Chen T Herman D Goodsaid F Hurban P Phillips K Xu J Deng X Sun Y Tong W Dragan Y Shi L "Rat toxicogenomic study reveals analytical consistency across microarray platforms" Nature Biotechnology 2006 24 1162 10.1038/ nbt1238 17061323
-
(2006)
Nature Biotechnology
, vol.24
, pp. 1162
-
-
Guo, L.1
Lobenhofer, E.2
Wang, C.3
Shippy, R.4
Harris, S.5
Zhang, L.6
Mei, N.7
Chen, T.8
Herman, D.9
Goodsaid, F.10
Hurban, P.11
Phillips, K.12
Xu, J.13
Deng, X.14
Sun, Y.15
Tong, W.16
Dragan, Y.17
Shi, L.18
-
24
-
-
0035942271
-
"Significance analysis of microarrays applied to the ionizing radiation response"
-
33173 11309499 10.1073/pnas.091062498
-
Tusher V Tibshirani R Chu G "Significance analysis of microarrays applied to the ionizing radiation response" Proc Natl Acad Sci USA 2001 98 5116 33173 11309499 10.1073/pnas.091062498
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 5116
-
-
Tusher, V.1
Tibshirani, R.2
Chu, G.3
-
25
-
-
84874661101
-
"Transcript assignment for Affymetrix GeneChip probe arrays"
-
Affymetrix Inc
-
Affymetrix Inc "Transcript assignment for Affymetrix GeneChip probe arrays" 2004 http://www.affymetrix.com/support/technical/ whitepapers/netaffxannot_whitepaper.pdf
-
(2004)
-
-
-
26
-
-
13444304325
-
NCBI GEO: Mining millions of expression profiles-database and tools
-
539976 15608262 10.1093/nar/gki022
-
Barrett T Suzek T Troup D Wilhite S Ngau W-C Ledoux P Rudnev D Lash A Fujibuchi W Edgar R NCBI GEO: Mining millions of expression profiles-database and tools Nucleic Acids Research 2005 33 D562 539976 15608262 10.1093/nar/gki022
-
(2005)
Nucleic Acids Research
, vol.33
-
-
Barrett, T.1
Suzek, T.2
Troup, D.3
Wilhite, S.4
Ngau, W.-C.5
Ledoux, P.6
Rudnev, D.7
Lash, A.8
Fujibuchi, W.9
Edgar, R.10
-
27
-
-
33645756545
-
"Bioinformatics and Computational Biology Solutions using R and Bioconductor"
-
Springer
-
Gentleman R Carey V Huber W Irizarry R Dudoit S "Bioinformatics and Computational Biology Solutions using R and Bioconductor" Springer 2005
-
(2005)
-
-
Gentleman, R.1
Carey, V.2
Huber, W.3
Irizarry, R.4
Dudoit, S.5
-
28
-
-
0037316303
-
"A comparison of normalization methods for high density oligonucleotide array data based on bias and variance"
-
10.1093/bioinformatics/19.2.185 12538238
-
Bolstad B Irizarry R Astrand M Speed T "A comparison of normalization methods for high density oligonucleotide array data based on bias and variance" Bioinformatics 2003 19 2 185-193 10.1093/ bioinformatics/19.2.185 12538238
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 185-193
-
-
Bolstad, B.1
Irizarry, R.2
Astrand, M.3
Speed, T.4
-
29
-
-
0037200201
-
"A new non-linear normalisation method for reducing variability in DNA microarray experiments"
-
0048 10.1186/gb-2002-3-9-research0048
-
Workman C Jensen L Jarmer H Berka R Gautier L Nielsen H Saxild H Nielsen C Brunak S Knudsen S "A new non-linear normalisation method for reducing variability in DNA microarray experiments" Genome Biology 2002 3 9 0048 10.1186/gb-2002-3-9-research0048
-
(2002)
Genome Biology
, vol.3
, Issue.9
-
-
Workman, C.1
Jensen, L.2
Jarmer, H.3
Berka, R.4
Gautier, L.5
Nielsen, H.6
Saxild, H.7
Nielsen, C.8
Brunak, S.9
Knudsen, S.10
-
30
-
-
0036356994
-
"Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays"
-
research0005.1 0005.10 10.1186/gb-2001-3-1-research0005
-
Chudin E Walker R Kosaka A Wu S Rabert D Chang T Kreder D "Assessment of the relationship between signal intensities and transcript concentration for Affymetrix GeneChip arrays" Genome Biology 2001 3 1 research0005.1 0005.10 10.1186/gb-2001-3-1-research0005
-
(2001)
Genome Biology
, vol.3
, Issue.1
-
-
Chudin, E.1
Walker, R.2
Kosaka, A.3
Wu, S.4
Rabert, D.5
Chang, T.6
Kreder, D.7
-
31
-
-
27644507562
-
"Microarray scanner calibration curves: Characteristics and implications"
-
1637029 16026596 10.1186/1471-2105-6-S2-S11
-
Shi L Tong W Su Z Han T Han J Puri R Fang H Frueh F Goodsaid F Guo L Branham W Chen J Xu Z Harris S Hong H Xie Q Perkins R Fuscoe J "Microarray scanner calibration curves: Characteristics and implications" BMC Bioinformatics 2005 6 Suppl 2 S11 1637029 16026596 10.1186/1471-2105-6-S2-S11
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 2
-
-
Shi, L.1
Tong, W.2
Su, Z.3
Han, T.4
Han, J.5
Puri, R.6
Fang, H.7
Frueh, F.8
Goodsaid, F.9
Guo, L.10
Branham, W.11
Chen, J.12
Xu, Z.13
Harris, S.14
Hong, H.15
Xie, Q.16
Perkins, R.17
Fuscoe, J.18
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