Iterative rank-order normalization of gene expression microarray data

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Welsh, Eric A ^a   Eschrich, Steven A ^a   Berglund, Anders E ^a   Fenstermacher, David A ^a  

^a H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

Affymetrix; Expression; GeneChip; Microarray; Normalization

Indexed keywords

AFFYMETRIX; EXPRESSION; EXPRESSION ANALYSIS; GENE EXPRESSION MICROARRAY; GENECHIPS; MODEL-BASED ESTIMATION; NORMALIZATION; SOFTWARE IMPLEMENTATION;

ESTIMATION; GENE EXPRESSION; IRON; IRON COMPOUNDS; MICROARRAYS; SIGNAL PROCESSING;

ITERATIVE METHODS;

ALGORITHM; ARTICLE; ARTIFACT; COMPUTER PROGRAM; DNA MICROARRAY; GENE EXPRESSION PROFILING; METHODOLOGY;

ALGORITHMS; ARTIFACTS; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 84877026600     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-153     Document Type: Article

References (20)

1. Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 2007, 8(1):118-127. 10.1093/biostatistics/kxj037, 16632515.
2. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207. 10.1093/nar/30.1.207, 99122, 11752295.
3. Parkinson H, Sarkans U, Kolesnikov N, Abeygunawardena N, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Holloway E. ArrayExpress update-an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res 2011, 39(suppl 1):D1002. 3013660, 21071405.
4. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249. 10.1093/biostatistics/4.2.249, 12925520.
5. Affymetrix Statistical algorithms description document 2002, Santa Clara, CA: Affymetrix Inc, Technical paper, Affymetrix.
6. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001, 2(8):research0032. 55329, 11532216.
7. Choe SE, Boutros M, Michelson AM, Church GM, Halfon MS. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 2005, 6(2):R16. 10.1186/gb-2005-6-2-r16, 551536, 15693945.
8. Irizarry RA, Wu Z, Jaffee HA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics (Oxford, England) 2006, 22(7):789-794.
9. Giorgi F, Bolger A, Lohse M, Usadel B. Algorithm-driven Artifacts in median polish summarization of Microarray data. BMC Bioinforma 2010, 11(1):553.
10. Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (Oxford, England) 2004, 20(3):323.
11. Calza S, Valentini D, Pawitan Y. Normalization of oligonucleotide arrays based on the least-variant set of genes. BMC Bioinforma 2008, 9(1):140.
12. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res 2003, 31(4):e15-e15. 10.1093/nar/gng015, 150247, 12582260.
13. International Genomics Consortium -- expO http://www.intgen.org/expo.
14. Fenstermacher DA, Wenham RM, Rollison DE, Dalton WS. Implementing personalized medicine in a cancer center. Cancer J 2011, 17(6):528. 10.1097/PPO.0b013e318238216e, 3240816, 22157297.
15. Eschrich SA, Hoerter AM, Bloom GC, Fenstermacher DA. Tissue-specific RMA models to incrementally normalize Affymetrix GeneChip data. Engineering in Medicine and Biology Society, 2008 EMBS 2008 30th Annual International Conference of the IEEE: 2008 2008, 2419-2422. IEEE.
16. Katz S, Irizarry R, Lin X, Tripputi M, Porter M. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC Bioinforma 2006, 7(1):464.
17. Eschrich SA, Hoerter AM. Libaffy: software for processing Affymetrix (R) GeneChip (R) data. Bioinformatics (Oxford, England) 2007, 23(12):1562-1564.
18. Cleveland WS. Robust locally weighted regression and smoothing scatterplots. J Am Stat Assoc 1979, 74(368):829-836.
19. Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J-C, Müller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinforma 2011, 12(1):77.
20. Affycomp III http://affycomp.biostat.jhsph.edu.