Chapter 5 Reproducibility of microarray studies: concordance of current analysis methods

Progress in Brain Research

Volumn 158, Issue , 2006, Pages 109-125

  Wayland, Matt T ^a   Bahn, Sabine ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BRAIN; COMPARATIVE STUDY; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMICS; HUMAN; METHODOLOGY; PHYSIOLOGY; QUALITY CONTROL; REPRODUCIBILITY; REVIEW; STANDARD;

ANIMALS; BRAIN; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; QUALITY CONTROL; REPRODUCIBILITY OF RESULTS;

EID: 33749257338     PISSN: 00796123     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6123(06)58005-7     Document Type: Review

References (41)

1. Affymetrix. (2002). Statistical algorithms description document. Technical report. www.affymetrix.com.
2. Affymetrix. (2004). Affymetrix genechip expression analysis: data analysis fundamentals. Technical report. www.affymetrix.com.
3. Affymetrix. (2005). Guide to probe logarithmic intensity error (plier) estimation. Technical report. www.affymetrix.com.
4. Benjamini Y., and Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57 (1995) 289-300
5. Blalock E.M., Geddes J.W., Chen K.C., Porter N.M., Markesbery W.R., and Landfield P.W. Incipient Alzheimer's disease: microarray correlation analyses reveal major transcriptional and tumour suppressor responses. Proc. Natl. Acad. Sci. USA 101 7 (2004) 2173-2178
6. Bolstad, B. (2004) Affyplm: methods for fitting probe level models to affy data. Technical report. www.bioconductor.org.
7. Chen D., Ma H., Hong H., Koh S.S., Huang S.M., Schurter B.T., Aswad D.W., and Stallcup M.R. Regulation of transcription by a protein methyltransferase. Science 284 (1999) 2174-2177
8. Choe S.E., Boutros M., Michelson A.M., Church G.M., and Halfon M.S. Preferred analysis methods for affymetrix genechips revealed by a wholly defined control dataset. Genome Biol. 6 (2005) R16
9. Cope L.M., Irizarry R.A., Jaffee H.A., Wu Z., and Speed T.P. A benchmark for affymetrix genechip expression measures. Bioinformatics 20 (2004) 323-331
10. Dai M., Wang P., Boyd A.D., Kostov G., Athey B., Jones E.G., Bunney W.E., Myers R.M., Speed T.P., Akil H., Watson S.J., and Meng F. Evolving gene/transcript definitions significantly alter the interpretation of genechip data. Nucleic Acids Res. 33 (2005) e175
11. Folstein M., Folstein S., and McHugh P. Mini-mental state a practical method for grading the cognitive state of patients for the clinician. J. Psychiatr. Res. 12 (1975) 189-198
12. Garge N.R., Page G.P., Sprague A.P., Gorman B.S., and Allison D.B. Reproducible clusters from microarray research: whither?. BMC Bioinform. 6 (2005) S10
13. Gautier L., Cope L., Bolstad B.M., and Irizarry R.A. affy - analysis of affymetrix genechip data at the probe level. Bioinformatics 20 3 (2004) 307-315
14. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Li F.L.C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y.H., and Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5 (2004) R80
15. Hollingshead D., Lewis D.A., and Mirnics K. Platform influence on DNA microarray data in postmortem brain research. Neurobiol. Dis. 18 3 (2005) 649-655
16. Huber W., von Heydebreck A., Sultmann H., Poustka A., and Vingron M. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioformatics 18 (2002) S96-S104
17. Irizarry R.A., Hobbs B., Collin F., Beazer-Barday Y.D., Antonellis K.J., Schery U., and Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4 2 (2003) 249-264
18. Irizarry, R.A., Wu, Z. and Jaffee, H.A. (2005) Comparison of affymetrix genechip expression measures. Johns Hopkins University, Dept. of Biostatistics Working Papers, Working Paper 86: 1-7.
19. Jackson E.S., Wayland M.T., Fitzgerald W., and Bahn S. A microarray data analysis framework for postmortem tissues. Methods 37 (2005) 247-260
20. Khatri P., Draghici S., Ostermeier C., and Krawetz S. Profiling gene expression utilizing onto-express. Genomics 79 (2002) 266-270
21. Khatri P., and Draghici S. Ontological analysis of gene exression data: current tools, limitations, and open problems. Bioinformatics 21 18 (2005) 3587-3595
22. Lehtovirta M., Kyttala A., Eskelinen E.L., Hess M., Heinonen O., and Jalanko A. Palmitoyl protein thioesterase (ppt) localizes into synaptosomes and synaptic vesicles in neurons: implications for infantile neuronal ceroid lipofuscinosis (incl). Hum. Mol. Genet. 10 (2001) 69-75
23. Lin, S.M. and Johnson. K.F. (2003) Correlation and Association Analysis, Chap. 17. Kluwer, Dordrecht, The Netherlands, pp. 289-305.
24. Jeanette N.M., Jerome R.E., Nicholson C.R., Crabb D.W., and Edenberg H.J. Reproducibility of oligonucleotide arrays using small samples. BMC Genom. 4 1 (2003) 4
25. Mutter G.L., Zahrieh D., Liu C., Neuberg D., Finkelstein D., Baker H.E., and Warrington J.A. Comparison of frozen and rnalater solid tissue storage methods for use in rna expression microarrays. BMC Genom. 5 (2004) 88
26. Pavlidis P. Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31 (2003) 282-289
27. Petalidis L., Bhattacharyya S., Morris G.A., Collins V.P., Freeman T.C., and Lyons P.A. Global amplification of mRNA by template-switching pcr: linearity and application to microarray analysis. Nucleic Acids Res. 31 22 (2003) e142
28. Petersen D., Chandramouli G.V.R., Geoghegan J., Hilburn J., Paarlberg J., Kim C.H., Munroe D., Gangi L., Han J., Puri R., Staudt L., Weinstein J., Barrett J.C., Green J., and Kawasaki E.S. Three microarray platforms: an analysis of their concordance in profiling gene expression. BMC Genom. 6 (2005) 63
29. Prabakaran S., Swatton J.E., Ryan M.M., Huffaker S.J., Huang J.T.-J., Griffin J.L., Wayland M., Freeman T., Dudbridge F., Lilley K.S., Karp N.A., Hester S., Tkachev D., Mimmack M.L., Yolken R.H., Webster M.J., Torrey E.F., and Bahn S. Mitochondrial dysfunction in schizophrenia: evidence for compromised brain metabolism and oxidative stress. Mol. Psychiatry 9 7 (2004) 684-697
30. R Development Core Team. (2005) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0.
31. Ryan M.M., Huffaker S.J., Webster M.J., Wayland M., Freeman T., and Bahn S. Application and optimization of microarray technologies for human postmortem brain studies. Biol. Psychiatry 55 4 (2004) 329-336
32. Shedden K., Chen W., Kuick R., Ghosh D., Macdonald J., Cho K.R., Giordano T.J., Gruber S.B., Fearon E.R., Taylor J.M.G., and Hanash S. Comparison of seven methods for producing affymetrix expression scores based on false discovery rates in disease profiling data. BMC Bioinform. 6 (2005) 26
33. Shippy R., Sendera T.J., Lockner R., Palaniappan C., Kaysser-Kranich T., Watts G., and Alsobrook J. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genom. 5 (2004) 61
34. Smyth, G.K. (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments, Stat. Appl. Genet. Mol. Biol., 3(1): Article 3. Available at: http://www.bepress.com/Sagmb/vol3/issi/art3.
35. Storey J.D. The positive false discovery rate: a Bayesian interpretation and the q-value. Ann. Stat. 31 6 (2003) 2013-2035
36. Storey J.D., and Tibshirani R. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. 100 16 (2003) 9440-9445
37. Wilson C.L., Pepper S.D., Hey Y., and Miller C.J. Amplification protocols introduce systematic but reproducible errors into gene expression studies. Biotechniques 36 3 (2004) 498-506
38. Wu, H. (2005). with ideas from Gary Churchill, Katie Kerr, and Xiangqin Cui. maanova: tools for analyzing Micro Array experiments. R package version 0.98.8.
39. Wu Z., and Irizarry R.A. Stochastic models inspired by hybridisation theory for short oligonucleotide arrays. J. Comput Biol. 12 6 (2005) 882-893
40. Wu, Z., Irizarry, R.A., Gentleman, R., Martinez Murillo, F., Spencer, F. (2003). A Model Based Background Adjustement for Oligonucleotide Expression Arrays. To appear in JASA.
41. Zakharkin S.O., Kim K., Mehta T., Chen L., Barnes S., Parrish R.S., Scheirer K.E., Allison D.B., and Page G.P. Sources of variation in affymetrix microarray experiments. BMC Bioinform. 6 (2005) 214