A Two-Stage Procedure for the Removal of Batch Effects in Microarray Studies

Statistics in Biosciences

Volumn 6, Issue 1, 2014, Pages 73-84

  Giordan, Marco ^a  

^a UNIVERSITY OF PADOVA   (Italy)

Author keywords

Bagging; Gene expression profiling; High dimensional data; Normalization

Indexed keywords

ARTICLE; GENE EXPRESSION PROFILING; HUMAN; INFORMATION SYSTEM; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PARAMETRIC TEST; PRIORITY JOURNAL; PROCESS MODEL; REGRESSION ANALYSIS; SAMPLE SIZE; SIMULATION; STANDARDIZATION; STATISTICAL DISTRIBUTION; VALIDATION PROCESS;

ZIZIPHUS MAURITIANA;

EID: 84899962802     PISSN: 18671764     EISSN: 18671772     Source Type: Journal    
DOI: 10.1007/s12561-013-9081-1     Document Type: Article

References (23)

1. Barnett S (1990) Matrices: methods and applications. Oxford University Press, Oxford.
2. Benito M, Parker J, Du Q, Xiang D, Perou CM, Marron JS (2004) Adjustment of systematic microarray data biases. Bioinformatics 20(1): 105-114. doi: 10. 1093/bioinformatics/btg385.
3. Breiman L (1996) Bagging predictors. Mach Learn 24(2): 123-140. doi: 10. 1023/A: 1018054314350.
4. Chen C, Grennan K, Badner J, Zhang D, Gershon E, Jin L, Liu C (2011) Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS ONE 6(2): e17238. 10. 1371/journal. pone. 0017238.
5. Davis S, Meltzer PS (2007) GEOquery: a bridge between the Gene Expression Omnibus (GEO) and bioconductor. Bioinformatics 23(14): 1846-1847. doi: 10. 1093/bioinformatics/btm254.
6. Efron B (2004) Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. J Am Stat Assoc 99(465): 96-104. doi: 10. 1198/016214504000000089.
7. Glejser H (1969) A new test for heteroskedasticity. J Am Stat Assoc 64(325): 316-323.
8. Huber WE, von Heydebreck A, Sultmann H, Poustka A, Vingron M (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18(1): S96-S104.
9. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2): 249-264.
10. Joe H (2006) Generating random correlation matrices based on partial correlations. J Multivar Anal 97: 2177-2189.
11. Johnson WE, Li C, Rabinovic A (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8(1): 118-127. doi: 10. 1093/biostatistics/kxj037.
12. Kohlmann A, Bullinger L, Thiede C, Schaich M, Schnittger S, Döhner K, Dugas M, Klein HU, Döhner H, Ehninger G, Haferlach T (2010) Gene expression profiling in AML with normal karyotype can predict mutations for molecular markers and allows novel insights into perturbed biological pathways. Leukemia 24: 1216.
13. 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 (2010) A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. Pharmacogenomics J. 10: 278-291.
14. McCall MN, Bolstad BM, Irizarry MA (2010) Frozen robust multiarray analysis (fRMA). Biostatistics 11(2): 242-253. doi: 10. 1093/biostatistics/kxp059.
15. McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA (2011) The gene expression barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res 39: D1011-D1015. doi: 10. 1093/nar/gkq1259.
16. Mecham BH, Nelson PS, Storey JD (2010) Supervised normalization of microarrays. Bioinformatics 26(10): 1308-1315. doi: 10. 1093/bioinformatics/btq118.
17. Schäfer J, Strimmer K (2005) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21(6): 754-764. doi: 10. 1093/bioinformatics/bti062.
18. Schäfer J, Strimmer K (2005) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol 4(1): 32. doi: 10. 2202/1544-6115. 1175.
19. Shabalin AA, Tjelmeland H, Fan C, Perou CM, Nobel AB (2008) Merging two gene-expression studies via cross-platform normalization. Bioinformatics 24(9): 1154-1160. doi: 10. 1093/bioinformatics/btn083.
20. Slawski M, Daumer M, Boulesteix AL (2008) CMA-a comprehensive bioconductor package for supervised classification with high dimensional data. BMC Bioinform 9: 439. doi: 10. 1186/1471-2105-9-439.
21. Sotiriou C, Wirapati P, Loi S, Harris A, Fox S, Smeds J, Nordgren H, Farmer P, Praz V, Haibe-Kains B, Desmedt C, Larsimont D, Cardoso F, Peterse H, Nuyten D, Buyse M, de Vijver MJV, Bergh J, Piccart M, Delorenzi M G (2006) Expression profiling in breast cancer: understanding the molecular basis of histologic grade to improve prognosis. J Natl Cancer Inst 98(4): 262-272. doi: 10. 1093/jnci/djj052.
22. Strimmer K (2008) A unified approach to false discovery rate estimation. BMC Bioinform 9: 303. doi: 10. 1186/1471-2105-9-303.
23. Zilliox MJ, Irizarry RA (2007) A gene expression barcode for microarray data. Nat Methods 4: 911-913. doi: 10. 1038/nmeth1102.