Reproducibility of microarray data: A further analysis of microarray quality control (MAQC) data

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Chen, James J ^a   Hsueh, Huey Miin ^b   Delongchamp, Robert R ^c   Lin, Chien Ju ^a   Tsai, Chen An ^d  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

^b NATIONAL CHENGCHI UNIVERSITY   (Taiwan)

^c UNIVERSITY OF ARKANSAS FOR MEDICAL SCIENCES   (United States)

^d CHINA MEDICAL UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

CORRELATION COEFFICIENT; DATA ANALYSIS METHODS; HIERARCHICAL CLUSTER ANALYSIS; MICROARRAY GENE EXPRESSION; MICROARRAY GENE EXPRESSION DATA; MULTIPLE PLATFORMS; REGULATORY DECISIONS; TAQMAN TECHNOLOGIES;

CLUSTER ANALYSIS; HIERARCHICAL SYSTEMS; QUALITY CONTROL;

GENE EXPRESSION;

ACCURACY; ANALYSIS OF VARIANCE; ANALYTICAL ERROR; ARTICLE; BIOINFORMATICS; CLUSTER ANALYSIS; CONTROLLED STUDY; CORRELATION COEFFICIENT; DATA ANALYSIS; DNA MICROARRAY; GENE EXPRESSION; INTERMETHOD COMPARISON; PROCESS OPTIMIZATION; QUALITY CONTROL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL SIGNIFICANCE; DNA PROBE; EQUIPMENT; GENE EXPRESSION PROFILING; GENETIC DATABASE; INSTRUMENTATION; LABORATORY DIAGNOSIS; METHODOLOGY; PROTEIN MICROARRAY; REGRESSION ANALYSIS; STANDARD; VALIDATION STUDY;

CLUSTER ANALYSIS; DATABASES, GENETIC; DNA PROBES; EQUIPMENT FAILURE ANALYSIS; FALSE POSITIVE REACTIONS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEIN ARRAY ANALYSIS; QUALITY CONTROL; REFERENCE STANDARDS; REGRESSION ANALYSIS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY;

EID: 38349088960     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-412     Document Type: Article

References (21)

1. Tan PK Downey TJ Spitznagel EL Xu P Fu D Dimitrov DS Lempicki RA Raaka BM Cam MC Evaluation of gene expression measurements from commercial microarray platforms Nucleic Acids Res 2003, 31:5676-5684 14500831 10.1093/nar/gkg763 206463
2. Irizarry RA Warren D Spencer F Kim IF Biswal S Frank BC Gabrielson E Garcia JG 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 Nat Methods 2005, 2:345-350 15846361 10.1038/nmeth756
3. Larkin JE Frank BC Gavras H Sultana R Quackenbush J Independence and reproducibility across microarray platforms Nat Methods 2005, 2:337-344 15846360 10.1038/nmeth757
4. Members of the Toxicogenomics Research Consortium Standardizing global gene expression analysis between laboratories and across platforms Nat Methods 2005, 2:351-356 15846362 10.1038/nmeth754
5. 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 JM 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 Clin Cancer Res 2005, 11(2 Pt 1):565-572 15701842
6. Ioannidis JP Microarrays and molecular research: Noise discovery? Lancet 2005, 365:454-455 15705441
7. Frantz S An array of problems Nat Rev Drug Discov 2005, 4:362-363 15902768 10.1038/nrd1746
8. Marshall E Getting the noise out of gene arrays Science 2004, 306:630-631 15499004 10.1126/science.306.5696.630
9. MAQC Consortium The MicroArray Quality Control (MAQC) project shows interplatform reproducibility of gene expression measurements Nature Biotechnology 2006, 24(9):1151-1161 16964229 10.1038/nbt1239
10. MAQC projet http://www.fda.gov/nctr/science/centers/toxicoinformatics/ maqc/
11. Perket JM Six things you won't find in the MAQC The Scientist 2006, 20(11):68-72
12. Klebanov L Qiu X Welle S Yakovlev A Statistical methods and microarray data Nat Biotechnol 2007, 25:25-26 17211383 10.1038/nbt0107-25
13. Shi L Jones WD Jensen RV Wolfinger RD Kawasaki ES Herman D Guo L Goodsaid FM Tong W Reply to Statistical methods and microarray data Nat Biotechnol 2007, 25:26-27 10.1038/nbt1322
14. Liang P MAQC papers over the cracks Nat Biotechnol 2007, 25:27-28 17211385 10.1038/nbt0107-27
15. Shi L Jones WD Jensen RV Wolfinger RD Kawasaki ES Herman D Guo L Goodsaid FM Tong W Reply to MAQC papers over the cracks Nat Biotechnol 2007, 25:28-29 10.1038/nbt1322
16. Guo L Lobenhofer EK Wang C Shippy R Harris SC Zhang L Mei N Chen T Herman D Goodsaid FM Hurban P Phillips KL Xu J Deng X Sun YA Tong W Dragan YP Shi L Rat toxicogenomic study reveals analytical consistency across microarray platforms Nat Biotechnol 2006, 24:1162-1169 17061323 10.1038/nbt1238
17. Benjamini Y Hochberg Y Controlling the false discovery rate - a practical and powerful approach to multiple testing J Roy Stat Soc B Met 1995, 57:289-300
18. Draghici S Khatri P Eklund AC Szallasi Z Reliability and reproducibility issues in DNA microarray measurements Trends Genet 2006, 22:101-109 16380191 10.1016/j.tig.2005.12.005
19. Canales RD Luo Y Willey JC Austermiller B Barbacioru CC Boysen C Hunkapiller K Jensen RV Knight CR Lee KY Ma Y Maqsodi B Papallo A Peters EH Poulter K Ruppel PL Samaha RR Shi L Yang W Zhang L Goodsaid FM Evaluation of DNA microarray results with alternative quantitative technology platforms Nat Biotechnol 2006, 24:1115-1122 16964225 10.1038/ nbt1236
20. Patterson TA Lobenhofer EK Fulmer-Smentek SB Collins PJ Chu TM Bao W Fang H Kawasaki ES Hager J Tikhonova IR Walker SJ Zhang L Hurban P de Longueville F Fuscoe JC Tong W Shi L Wolfinger RD Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project Nat Biotechnol 2006, 24:1140-1149 16964228 10.1038/nbt1242
21. Chow SC Liu JP Design and Analysis of Bioavailability and Bioequivalence Studies Marcel DFekker, New York 1992