Erratum: IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics (Bioinformatics (2014) 30:10 (1392-1399) DOI: 10.1093/bioinformatics/btu027));IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics

Bioinformatics

Volumn 30, Issue 10, 2014, Pages 1392-1399

  Rosikiewicz, Marta ^a,b   Robinson Rechavi, Marc ^a,b  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOMETRY; DNA MICROARRAY; GENE EXPRESSION PROFILING; HUMAN; METHODOLOGY; QUALITY CONTROL; REPRODUCIBILITY;

ALGORITHMS; ANIMALS; BENCHMARKING; BIOMETRY; GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS;

EID: 84900819430     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw374     Document Type: Erratum

References (39)

1. Affymetrix. (2001) Guidelines for assessing data quality. Affymetrix Inc, Santa Clara, C.A.
2. Asare, A.L. et al. (2009) Power enhancement via multivariate outlier testing with gene expression arrays. Bioinformatics, 25, 48-53
3. Bastian, F. et al. (2008) Bgee: Integrating and comparing heterogeneous transcriptome data among species. In: Bairoch, A., Cohen-Boulakia, S. and Froidevaux, C. (eds) Data Integration in the Life Sciences. Springer, Berlin, Heidelberg, pp. 124-131
4. Beisvag, V. et al. (2011) Contributions of the EMERALD project to assessing and improving microarray data quality. Biotechniques, 50, 27-31
5. Bolstad, B.M. et al. (2005) Quality assessment of Affymetrix GeneChip data. In: Gentleman, R., et al. (eds) Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Springer, New York, pp. 33-47
6. Bolstad, B.M. et al. (2004) Experimental design and low-level analysis of microarray data. Int. Rev. Neurobiol., 60, 25-58
7. Brawand, D. et al. (2011) The evolution of gene expression levels in mammalian organs. Nature, 478, 343-348
8. Brazma, A. et al. (2003) ArrayExpress-A public repository for microarray gene expression data at the EBI. Nucleic Acids Res., 31, 68-71
9. Brettschneider, J. et al. (2008) Quality assessment for short oligonucleotide microarray data. Technometrics, 50, 241-264
10. Canales, R.D. et al. (2006) Evaluation of DNA microarray results with quantitative gene expression platforms. Nat. Biotechnol., 24, 1115-1122
11. Dash, S. et al. (2012) PLEXdb: Gene expression resources for plants and plant pathogens. Nucleic Acids Res., 40, D1194-D1201
12. Edgar, R., Domrachev, M. and Lash, A.E. (2002) Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res., 30, 207-210
13. Flicek, P. et al. (2013) Ensembl 2013. Nucleic Acids Res., 41, D48-D55
14. Gagnon-Bartsch, J.A. and Speed, T.P. (2012) Using control genes to correct for unwanted variation in microarray data. Biostatistics, 13, 539-552
15. Gautier, L. et al. (2004) affy-Analysis of Affymetrix GeneChip data at the probe level. Bioinformatics, 20, 307-315
16. Gentleman, R.C. et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol., 5, R80
17. Hebestreit, K. et al. (2012) Leukemia gene atlas-A public platform for integrative exploration of genome-wide molecular data. PLoS One, 7, e39148
18. Hruz, T. et al. (2008) Genevestigator v3: A reference expression database for the meta-Analysis of transcriptomes. Adv. Bioinform., 2008, 420747
19. Irizarry, R.A. et al. (2003) Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res., 31, e15
20. Irizarry, R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264
21. Kapushesky, M. et al. (2010) Gene expression atlas at the European bioinformatics institute. Nucleic Acids Res., 38, D690-D698
22. Kauffmann, A., Gentleman, R. and Huber, W. (2009) arrayQualityMetrics-A bioconductor package for quality assessment of microarray data. Bioinformatics, 25, 415-416
23. Kauffmann, A. and Huber, W. (2010) Microarray data quality control improves the detection of differentially expressed genes. Genomics, 95, 138-142
24. Le Crom, S. et al. (2002) yMGV: Helping biologists with yeast microarray data mining. Nucleic Acids Res., 30, 76-79
25. Lockhart, D.J. et al. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol., 14, 1675-1680
26. McCall, M.N., Bolstad, B.M. and Irizarry, R.A. (2010) Frozen robust multiarray analysis (fRMA). Biostatistics, 11, 242-253
27. McCall, M.N. et al. (2011) Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics, 12, 137
28. Novak, J.P., Sladek, R. and Hudson, T.J. (2002) Characterization of variability in large-scale gene expression data: Implications for study design. Genomics, 79, 104-113
29. Obayashi, T. et al. (2013) COXPRESdb: A database of comparative gene coexpression networks of eleven species for mammals. Nucleic Acids Res., 41, D1014-D1020
30. Piasecka, B. et al. (2012) Comparative modular analysis of gene expression in vertebrate organs. BMC Genomics, 13, 124
31. Rhodes, D.R. et al. (2007) Oncomine 3.0: Genes, pathways, and networks in a collection of 18, 000 cancer gene expression profiles. Neoplasia, 9, 166-180
32. Shedden, K. et al. (2005) Comparison of seven methods for producing Affymetrix expression scores based on False Discovery Rates in disease profiling data. BMC Bioinformatics, 6, 26
33. Tseng, G.C., Ghosh, D. and Feingold, E. (2012) Comprehensive literature review and statistical considerations for microarray meta-Analysis. Nucleic Acids Res., 40, 3785-3799
34. Wilkes, T., Laux, H. and Foy, C.A. (2007) Microarray data quality-review of current developments. OMICS, 11, 1-13
35. Wilson, C.L. and Miller, C.J. (2005) Simpleaffy: A BioConductor package for Affymetrix Quality Control and data analysis. Bioinformatics, 21, 3683-3685
36. Wu, C., Macleod, I. and Su, A.I. (2013) BioGPS and MyGene.info: Organizing online, gene-centric information. Nucleic Acids Res., 41, D561-D565
37. Xiao, S.J. et al. (2010) TiSGeD: A database for tissue-specific genes. Bioinformatics, 26, 1273-1275
38. Zheng-Bradley, X. et al. (2010) Large scale comparison of global gene expression patterns in human and mouse. Genome Biol., 11, R124
39. Zhu, Y. et al. (2008) GEOmetadb: Powerful alternative search engine for the Gene Expression Omnibus. Bioinformatics, 24, 2798-2800.