Normalization of oligonucleotide arrays based on the least-variant set of genes

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Calza, Stefano ^a,b   Valentini, Davide ^a   Pawitan, Yudi ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

^b UNIVERSITY OF BRESCIA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

LINEAR MODELING; MICROARRAY DATA; NORMALIZATION METHODS; OLIGONUCLEOTIDE ARRAYS; REFERENCE SET; STANDARD ASSUMPTIONS;

OLIGONUCLEOTIDES;

GENES;

ARTICLE; DNA MICROARRAY; DOWN REGULATION; GENE IDENTIFICATION; HOUSEKEEPING GENE; SENSITIVITY ANALYSIS; STANDARD; STATISTICAL MODEL; UPREGULATION; ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE; GENE EXPRESSION PROFILING; GENETIC VARIABILITY; GENETICS; METHODOLOGY;

ALGORITHMS; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENES; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; VARIATION (GENETICS);

EID: 42449104860     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-140     Document Type: Article

References (36)

1. Hartemink A Gifford D Jaakkola T Young R Maximum likelihood estimation of optimal scaling factors for expression array normalizations IN SPIE Bios 2001.
2. Hoffmann R Seidl T Dugas M Profound effect of normalization on detection of differentially expressed genes in oligonucleotide microarray data analysis Genome Biol 2002, 3:7. research0033.1 0033.11 10.1186/ gb-2002-3-7-research0033
3. Workman C Jensen LJ Jarmer H Berka R Gautier L Nielser HB Saxild HH Nielsen C Brunak S Knudsen S A new non-linear normalization method for reducing variability in DNA microarray experiments Genome Biol 2002, 3:9, research0048. 126873 12225587 10.1186/gb-2002-3-9-research0048
4. Bolstad BM Irizarry RA Astrand M Speed TP A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/ 19.2.185 12538238
5. Affymetrix Statistical Algorithms Description Document 2002
6. Yang YH Dudoit S Luu P Lin DM Peng V Ngai J Speed TP Normalization for cDNA microarray data: A robust composite method addressing single and multiple slide systematic variation Nucleic Acids Res 2002, 30(4):e15. 100354 11842121 10.1093/nar/30.4.e15
7. Haslett JN Sanoudou D Kho AT Bennett RR Greenberg SA Kohane IS Beggs AH Kunkel LM Gene expression comparison of biopsies from Duchenne muscular dystrophy (DMD) and normal skeletal muscle Proc Natl Acad Sci USA 2002, 99(23):15000-5. 137534 12415109 10.1073/pnas.192571199
8. Ploner A Calza S Gusnanto A Pawitan Y Multidimensional local false discovery rate for microarray studies Bioinformatics 2006, 22(5):556-565. 10.1093/bioinformatics/btk013 16368770
9. Quackenbush J Microarray data normalization and transformation Nat Genet 2002, 32(Suppl): 496-501. 10.1038/ng1032 12454644
10. Choe S Boutros M Michelson A Church G Halfon M Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset Genome Biology 2005, 6(2):R16. 551536 15693945 10.1186/ gb-2005-6-2-r16
11. Porter JD Khanna S Kaminski HJ Rao JS Merriam AP Richmonds CR Leahy P Li J Guo W Andrade FH A chronic inflammatory response dominates the skeletal muscle molecular signature in dystrophin-deficient mdx mice Hum Mol Genet 2002, 11(3):263-272. 10.1093/hmg/11.3.263 11823445
12. Haslett JN Sanoudou D Kho AT Han M Bennett RR Kohane IS Beggs AH Kunkel LM Gene expression profiling of Duchenne muscular dystrophy skeletal muscle Neurogenetics 2003, 4(4):163-171. 10.1007/s10048-003-0148-x 12698323
13. Timmons JA Jansson E Fischer H Gustafsson T Greenhaff PL Ridden J Rachman J Sundberg CJ Modulation of extracellular matrix genes reflects the magnitude of physiological adaptation to aerobic exercise training in humans BMC Biol 2005, 3:19. 1224855 16138928 10.1186/1741-7007-3-19
14. Oshlack A Emslie D Corcoran LM Smyth GK Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes Genome Biol 2007, 8:R2. 1839120 17204140 10.1186/gb-2007-8-1-r2
15. Sturzenbaum SR Kille P Control genes in quantitative molecular biological techniques: The variability of invariance Comp Biochem Physiol B Biochem Mol Biol 2001, 130(3):281-289. 10.1016/ S1096-4959(01)00440-7 11567890
16. Bustin SA Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): Trends and problems J Mol Endocrinol 2002, 29:23-39. 10.1677/jme.0.0290023 12200227
17. Ermolaeva O Rastogi M Pruitt KD Schuler GD Bittner ML Chen Y Simon R Meltzer P Trent JM Boguski MS Data management and analysis for gene expression arrays Nat Genet 1998, 20:19-23. 10.1038/1670 9731524
18. Schmittgen TD Zakrajsek BA Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitative RT-PCR J Biochem Biophys Methods 2000, 46(1-2):69-81. 10.1016/ S0165-022X(00)00129-9 11086195
19. Glare EM Divjak M Bailey MJ Walters EH beta-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels Thorax 2002, 57(9):765-770. 10.1136/ thorax.57.9.765 12200519
20. Neuvians TP Gashaw I Sauer CG von Ostau C Kliesch S Bergmann M Hacker A Grobholz R Standardization strategy for quantitative PCR in human seminoma and normal testis J Biotechnol 2005, 117(2):163-171. 10.1016/ j.jbiotec.2005.01.011 15823405
21. Ploner A Miller LD Hall P Bergh J Pawitan Y Correlation test to assess low-level processing of high-density oligonucleotide microarray data BMC Bioinformatics 2005, 6:80. 1084343 15799785 10.1186/1471-2105-6-80
22. Schadt EE Li C Ellis B Wong WH Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data J Cell Biochem Suppl 2001, (Suppl 37):120-125. 10.1002/jcb.10073 11842437
23. Li C Wong WH Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection Proc Natl Acad Sci USA 2001, 98:31-36. 14539 11134512 10.1073/pnas.011404098
24. 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):249-254. 10.1093/biostatistics/4.2.249 12925520
25. Huber P Robust statistics John Wiley & Sons, Inc., New York 1981
26. Bolstad B affyPLM: Methods for fitting probe-level models 2006 [R package version 1.8.0]
27. Koenker R Bassett G Regression quantiles Econometrica 1978, 46:33-50. 10.2307/1913643
28. Koenker R quantreg: Quantile Regression 2007 http://www.r-project.org [R package version 4.06]
29. Affymetrix Support: Latin Square Data for Expression Algorithm Assessment http://www.affymetrix.com/support/technical/sample_data/ datasets.affx
30. Affycomp II: A Benchmark for Affymetrix GeneChip Expression Measures http://affycomp.biostat.jhsph.edu/
31. Cope LM Irizarry RA Jaffee HA Wu Z Speed TP A benchmark for Affymetrix GeneChip expression measures Bioinformatics 2004, 20(3):323-331. 10.1093/ bioinformatics/btg410 14960458
32. Smyth GK Linear models and empirical bayes methods for assessing differential expression in microarray experiments Stat Appl Genet Mol Biol 2004, 3. Article3 16646809
33. Irizarry RA Wu Z Cawley S affycomp: Graphics Toolbox for Assessment of Affymetrix Expression Measures 2005 [R package version 1.12.0]
34. Irizarry RA Wu Z Jaffee HA Comparison of Affymetrix GeneChip expression measures Bioinformatics 2006, 22(7):789-794. 10.1093/bioinformatics/ btk046 16410320
35. McGee M Chen Z New Spiked-In Probe Sets for the Affymetrix HGU-133A Latin Square Experiment COBRA Preprint Series 2006. Article 5 http://biostats.bepress.com/cobra/ps/art5
36. Parrish RS Spencer HJ Effect of normalization on significance testing for oligonucleotide microarrays J Biopharm Stat 2004, 14(3):575-579. 10.1081/BIP-200025650 15468753