Detection call algorithms for high-throughput gene expression microarray data

Briefings in Bioinformatics

Volumn 11, Issue 2, 2009, Pages 244-252

  Archer, Kellie J ^a   Reese, Sarah E ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

Author keywords

Detection calls; Gene expression; Microarray; Present

Indexed keywords

ALGORITHM; ARTICLE; DNA MICROARRAY; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENETIC DATABASE; HIGH THROUGHPUT SCREENING; METHODOLOGY;

ALGORITHMS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HIGH-THROUGHPUT SCREENING ASSAYS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SEQUENCE ANALYSIS, DNA;

EID: 77950937550     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbp055     Document Type: Article

References (39)

1. Hubbell E, Liu WM, Mei R. Robust estimators for expression analysis. Bioinformatics 2002;18:1585-1592.
2. Irizarry RA, Hobbs B, Collin F, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003;4:249-264.
3. Wu Z, Irizarry RA, Gentleman R, et al. A model-based background adjustment for oligonucleotide expression arrays. JAmStatAssoc 2004;99:909-917.
4. Li C, Wong WH. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error applications. Genome Biol 2001;2:1-11.
5. Shi L, Reid LH, Jones WD, et al. The MicroArray Quality Control (MAQC) project shows inter-and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006;24:1151-1161.
6. Hackstadt AJ, Hess AM. Filtering for increased power for microarray data analysis. BMC Bioinformatics 2009; 10:11.
7. Pepper SD, Saunders EK, Edwards LE, et al. The utility of MAS5 expression summary and detection call algorithms. BMC Bioinformatics 2007;8:273.
8. McClintick JN, Edenberg HJ. Effects of filtering by Present call on analysis of microarray experiments. BMC Bioinformatics 2006;7:49.
9. Ryan CA, Gildea LA, Hulette BC, et al. Gene expression changes in peripheral blood-derived dendritic cells following exposure to a contact allergen. Toxicol Lett 2004;150:301-316.
10. McClintick JN, Jerome RE, Nicholson CR, et al. Reproducibility of oligonucleotide arrays using small samples. BMCGenomics 2003;4:4.
11. Aston C, Jiang L, Sokolov BP. Transcriptional profiling reveals evidence for signaling and oligodendroglial abnormalities in the temporal cortex from patients with major depressive disorder. Mol Psychiatry 2005;10:309-322.
12. Shippy R, Sendera TJ, Lockner R, et al. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 2004;5:61.
13. Singh R, Maganti RJ, Jabba SV, et al. Microarray-based comparison of three amplification methods for nanogram amounts of total RNA. Am J Physiol Cell Physiol 2005;288:C1179-1189.
14. Dumur CI, Nasim S, Best AM, et al. Evaluation of qualitycontrol criteria for microarray gene expression analysis. Clin Chem 2004;50:1994-2002.
15. Mas VR, Archer KJ, Yanek K, et al. Gene expression patterns in deceased donor kidneys developing delayed graft function after kidney transplantation. Transplantation 2008;85:626-635.
16. Archer KJ, Mas VR, O'Brien TR, et al. Quality assessment of microarray data in a multicenter study. Diagn Mol Pathol 2009;18:34-43.
17. Weis S, Llenos IC, Dulay JR, et al. Quality control for microarray analysis of human brain samples: The impact of postmortem factors, RNA characteristics, and histopathology. J Neurosci Methods 2007;165:198-209.
18. Hoshida Y, Villanueva A, Kobayashi M, et al. Gene expression in fixed tissues and outcome in hepatocellular carcinoma. N Engl J Med 2008;359:1995-2004.
19. Mah N, Thelin A, Lu T, et al. A comparison of oligonucleotide and cDNA-based microarray systems. Physiol Genomics 2004;16:361-370.
20. Mahadevappa M, Warrington JA. A high-density probe array sample preparation method using 10-to 100-fold fewer cells. Nat Biotechnol 1999;17:1134-1136.
21. Seo J, Bakay M, Chen YW, et al. Interactively optimizing signal-to-noise ratios in expression profiling: projectspecific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics 2004;20: 2534-2544.
22. Stossi F, Barnett DH, Frasor J, et al. Transcriptional profiling of estrogen-regulated gene expression via estrogen receptor (ER) alpha or ERbeta in human osteosarcoma cells: distinct and common target genes for these receptors. Endocrinology 2004;145:3473-3486.
23. Frasor J, Stossi F, Danes JM, et al. Selective estrogen receptor modulators: discrimination of agonistic versus antagonistic activities by gene expression profiling in breast cancer cells. Cancer Res 2004;64:1522-1533.
24. Reme T, Hose D, De Vos J, et al. A new method for class prediction based on signed-rank algorithms applied to Affymetrix microarray experiments. BMC Bioinformatics 2008;9:16.
25. Lockhart DJ, Dong H, Byrne MC, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol 1996;14:1675-1680.
26. Schadt EE, Li C, Su C, et al. Analyzing high-density oligonucleotide gene expression array data. J Cell Biochem 2000;80:192-202.
27. Schadt EE, Li C, Ellis B, et al. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J Cell Biochem Suppl 2001;(Suppl 37):120-125.
28. Liu WM, Mei R, Di X, et al. Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 2002;18:1593-1599.
29. Kuhn K, Baker SC, Chudin E, et al. A novel, highperformance random array platform for quantitative gene expression profiling. Genome Res 2004;14: 2347-2356.
30. Illumina. BeadStudio Gene Expression Module v3.4 User Guide. http://www.illumina.com/downloads/BeadStudio_Gene_Expression_Module_v3.4_User_Guide_11317265_RevA.pdf (date last accessed 19 February 2009).
31. Illumina. Gene Expression Microarray Data Quality Control. http://www.illumina.com/downloads/GX_ QualityControl_TechNote.pdf (date last accessed 19 February 2009).
32. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002;30:207-210.
33. Dunning MJ, Barbosa-Morais NL, Lynch AG, et al. Statistical issues in the analysis of Illumina data. BMC Bioinformatics 2008;9:85.
34. Dunning MJ, Ritchie ME, Barbosa-Morais NL, et al. Spikein validation of an Illumina-specific variance-stabilizing transformation. BMC Res Notes 2008;1:18.
35. Dunning MJ, Smith ML, Ritchie ME, et al. beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 2007;23:2183-2184.
36. R Development Core Team. R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing, 2008.
37. Gautier L, Cope L, Bolstad BM, et al. affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004;20:307-315.
38. Wu C, Zhao H, Baggerly K, et al. Short oligonucleotide probes containing G-stacks display abnormal binding affinity on Affymetrix microarrays. Bioinformatics 2007;23:2566-2572.
39. Upton GJ, Langdon WB, Harrison AP. G-spots cause incorrect expression measurement in Affymetrix microarrays. BMCGenomics 2008;9:613.