Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Ambroise, Jérôme ^a   Bearzatto, Bertrand ^a   Robert, Annie ^a   Govaerts, Bernadette ^a   Macq, Benoît ^a   Gala, Jean Luc ^a  

^a UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BACKGROUND CORRECTION; BACKGROUND CORRECTION METHODS; COMPARISON STUDY; LOW-INTENSITY; MICROARRAY DATA; PRE-PROCESSING METHOD; PRE-PROCESSING STEP; TRANSFORMATION METHODS;

ESTIMATION;

METADATA;

ARTICLE; DNA MICROARRAY; GENE EXPRESSION PROFILING; HUMAN; METHODOLOGY; QUALITY CONTROL;

GENE EXPRESSION PROFILING; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL;

EID: 80054873254     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-413     Document Type: Article

References (31)

1. Hardiman G. Microarray platforms-comparisons and contrasts. Pharmacogenomics 2004, 5(5):487-502. 10.1517/14622416.5.5.487, 15212585.
2. Leung Y, Cavalieri D. Fundamentals of cDNA microarray data analysis. TRENDS in Genetics 2003, 19(11):649-659. 10.1016/j.tig.2003.09.015, 14585617.
3. Yang Y, Buckley M, Speed T. Analysis of cDNA microarray images. Briefings in bioinformatics 2001, 2(4):341. 10.1093/bib/2.4.341, 11808746.
4. Dudoit S, Yang Y, Callow M, Speed T. Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Statistica sinica 2002, 12:111-140.
5. Han T, Melvin C, Shi L, Branham W, Moland C, Pine P, Thompson K, Fuscoe J. Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions. BMC bioinformatics 2006, 7(Suppl 2):S17. 10.1186/1471-2105-7-S2-S17, 1764473, 17254301.
6. de Cremoux P, Valet F, Gentien D, Lehmann-Che J, Scott V, Tran-Perennou C, Barbaroux C, Servant N, Vacher S, Sigal-Zafrani B, Mathieu MC, Bertheau P, Guinebretiere JM, B A, Marty M, Spyrato S. Importance of pre-analytical steps for transcriptome and RT-qPCR analyses in the context of the phase II randomized multicentre trial REMAGUS02 of neoadjuvant chemotherapy in breast cancer patients. BMC cancer 2011, 11:215. 10.1186/1471-2407-11-215, 3126791, 21631949.
7. Cui X, Kerr M, Churchill G. Transformations for cDNA microarray data. Statistical applications in genetics and molecular biology 2003, 2:1009.
8. Quackenbush J. Microarray data normalization and transformation. nature genetics 2002, 32(supp):496-501. 10.1038/ng1032, 12454644.
9. Yang M, Ruan Q, Yang J, Eckenrode S, Wu S, McIndoe R, She J. A statistical method for flagging weak spots improves normalization and ratio estimates in microarrays. Physiological genomics 2001, 7:45.
10. Kooperberg C, Fazzio T, Delrow J, Tsukiyama T. Improved background correction for spotted DNA microarrays. Journal of Computational Biology 2002, 9:55-66. 10.1089/10665270252833190, 11911795.
11. Edwards D. Non-linear normalization and background correction in one-channel cDNA microarray studies. Bioinformatics 2003, 19(7):825. 10.1093/bioinformatics/btg083, 12724292.
12. Zhang D, Zhang M, Wells M. Multiplicative background correction for spotted microarrays to improve reproducibility. Genetics Research 2006, 87(03):195-206.
13. Scharpf R, Iacobuzio-Donahue C, Sneddon J, Parmigiani G. When should one subtract background fluorescence in 2-color microarrays?. Biostatistics 2007, 1-13.
14. Durbin B, Hardin J, Hawkins D, Rocke D. A variance-stabilizing transformation for gene-expression microarray data. Bioinformatics 2002, 18(suppl 1):S105. 10.1093/bioinformatics/18.suppl_1.S105, 12169537.
15. 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. 10.1093/bioinformatics/18.suppl_1.S96, 12169536.
16. Huber W, Von Heydebreck A, Sultmann H, Poustka A, Vingron M. Parameter estimation for the calibration and variance stabilization of microarray data. Statistical Applications in Genetics and Molecular Biology 2003, 2:1008.
17. Durbin B, Rocke D. Estimation of transformation parameters for microarray data. Bioinformatics 2003, 19(11):1360. 10.1093/bioinformatics/btg178, 12874047.
18. Ritchie M, Silver J, Oshlack A, Holmes M, Diyagama D, Holloway A, Smyth G. A comparison of background correction methods for two-colour microarrays. Bioinformatics-Oxford 2007, 23(20):2700.
19. Shi L, Reid L, Jones W, Shippy R, Warrington J, Baker S, Collins P, De Longueville F, Kawasaki E, Lee K, et al. The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nature biotechnology 2006, 24(9):1151-1161. 10.1038/nbt1239, 16964229.
20. Shippy R, Fulmer-Smentek S, Jensen R, Jones W, Wolber P, Johnson C, Pine P, Boysen C, Guo X, Chudin E, et al. Using RNA sample titrations to assess microarray platform performance and normalization techniques. Nature biotechnology 2006, 24(9):1123-1131. 10.1038/nbt1241, 16964226.
21. Gentleman R, Carey V, Bates D, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber H, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini A, Sawitzki G, Smith C, Smyth G, Tierney L, YH YJ, J Z. Bioconductor: open software development for computational biology and bioinformatics. Genome biology 2004, 5(10):R80. 10.1186/gb-2004-5-10-r80, 545600, 15461798.
22. Tran P, Peiffer D, Shin Y, Meek L, Brody J, Cho K. Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals. Nucleic Acids Research 2002, 30(12):e54. 10.1093/nar/gnf053, 117296, 12060692.
23. Lee G, Tillinghast J, Rocke D. LMGene User's Guide. dim (exprs (sample. eS) 2010, 1(613):32.
24. Barrett T, Edgar R. Gene Expression Omnibus (GEO): Microarray data storage, submission, retrieval, and analysis. Methods in enzymology 2006, 411:352. 1619900, 16939800.
25. Allison D, Cui X, Page G, Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nature Reviews Genetics 2006, 7:55-65. 10.1038/nrg1749, 16369572.
26. Smyth G. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical applications in genetics and molecular biology 2004, 3:1027.
27. Muller R, Buttner P. A critical discussion of intraclass correlation coefficients. Statistics in Medicine 1994, 13(23-24):2465-2476. 10.1002/sim.4780132310, 7701147.
28. Lin S, Du P, Huber W, Kibbe W. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Research 2008, 36(2):e11. 2241869, 18178591.
29. Tarca A, Romero R, Draghici S. Analysis of microarray experiments of gene expression profiling. American journal of obstetrics and gynecology 2006, 195(2):373-388. 10.1016/j.ajog.2006.07.001, 2435252, 16890548.
30. Patterson T, Lobenhofer E, Fulmer-Smentek S, Collins P, Chu T, Bao W, Fang H, Kawasaki E, Hager J, Tikhonova I, et al. Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project. Nature biotechnology 2006, 24(9):1140-1150. 10.1038/nbt1242, 16964228.
31. Parsons H, Ludwig C, Gunther U, Viant M. Improved classification accuracy in 1- and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation. BMC bioinformatics 2007, 8:234. 10.1186/1471-2105-8-234, 1965488, 17605789.