Home LiteratureArticle Details
PMID: 16356924 Published · epublish English Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't

Integrating probe-level expression changes across generations of Affymetrix arrays.

Nucleic acids research ·Vol. 33 ·No. 22 ·2005-12-14 ·Pages e193

Elo LL, Lahti L, Skottman H, Kyläniemi M, Lahesmaa R, Aittokallio T

Abstract

There is an urgent need for bioinformatic methods that allow integrative analysis of multiple microarray data sets. While previous studies have mainly concentrated on reproducibility of gene expression levels within or between different platforms, we propose a novel meta-analytic method that takes into account the vast amount of available probe-level information to combine the expression changes across different studies. We first show that the comparability of relative expression changes and the consistency of differentially expressed genes between different Affymetrix array generations can be considerably improved by determining the expression changes at the probe-level and by considering the latest information on probe-level sequence matching instead of the probe annotations provided by the manufacturer. With the improved probe-level expression change estimates, data from different generations of Affymetrix arrays can be combined more effectively. This will allow for the full exploitation of existing results when designing and analyzing new experiments.

MeSH Terms
Animals Cell Line Female Gene Expression Profiling/methods Humans Meta-Analysis as Topic Mice Mice, Inbred BALB C Oligonucleotide Array Sequence Analysis/methods Oligonucleotide Probes Reproducibility of Results Sample Size
Chemicals
Oligonucleotide Probes
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Elo Laura L
Department of Mathematics, FIN-20014, University of Turku, Finland. [email protected]
Lahti Leo
Skottman Heli
Kyläniemi Minna
Lahesmaa Riitta
Aittokallio Tero
References (33)
33 references, click to expand
  1. Combining Affymetrix microarray results.
    BMC Bioinformatics. 2005;6:57 PMID: 15774008
  2. Gene expression signatures of seven individual human embryonic stem cell lines.
    Stem Cells. 2005 Oct;23(9):1343-56 PMID: 16081666
  3. Sequence-matched probes produce increased cross-platform consistency and more reproducible biological results in microarray-based gene expression measurements.
    Nucleic Acids Res. 2004;32(9):e74 PMID: 15161944
  4. Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach.
    Genomics. 2005 Mar;85(3):297-308 PMID: 15718097
  5. Cross-study validation and combined analysis of gene expression microarray data.
    Biostatistics. 2008 Apr;9(2):333-54 PMID: 17873151
  6. BLAT--the BLAST-like alignment tool.
    Genome Res. 2002 Apr;12(4):656-64 PMID: 11932250
  7. Current issues for DNA microarrays: platform comparison, double linear amplification, and universal RNA reference.
    J Biotechnol. 2004 Sep 9;112(3):225-45 PMID: 15313001
  8. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer.
    Cancer Res. 2002 Aug 1;62(15):4427-33 PMID: 12154050
  9. Entrez Gene: gene-centered information at NCBI.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D54-8 PMID: 15608257
  10. A high performance test of differential gene expression for oligonucleotide arrays.
    Genome Biol. 2003;4(10):R67 PMID: 14519202
  11. Improving identification of differentially expressed genes in microarray studies using information from public databases.
    Genome Biol. 2004;5(9):R70 PMID: 15345054
  12. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
    Bioinformatics. 2003 Jan 22;19(2):185-93 PMID: 12538238
  13. Classification of pediatric acute lymphoblastic leukemia by gene expression profiling.
    Blood. 2003 Oct 15;102(8):2951-9 PMID: 12730115
  14. Combining gene expression data from different generations of oligonucleotide arrays.
    BMC Bioinformatics. 2004 Oct 25;5:159 PMID: 15504239
  15. Bioconductor: open software development for computational biology and bioinformatics.
    Genome Biol. 2004;5(10):R80 PMID: 15461798
  16. Local immune responses to Chlamydia pneumoniae in the lungs of BALB/c mice during primary infection and reinfection.
    Infect Immun. 1998 Nov;66(11):5113-8 PMID: 9784511
  17. Alternative mapping of probes to genes for Affymetrix chips.
    BMC Bioinformatics. 2004 Aug 14;5:111 PMID: 15310390
  18. Reproducibility of gene expression across generations of Affymetrix microarrays.
    BMC Bioinformatics. 2003 Jun 25;4:27 PMID: 12823866
  19. Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
    Stat Appl Genet Mol Biol. 2004;3:Article3 PMID: 16646809
  20. Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates.
    Bioinformatics. 2005 Jun 15;21(12):2861-6 PMID: 15814562
  21. Derivation of human embryonic stem cell lines in serum replacement medium using postnatal human fibroblasts as feeder cells.
    Stem Cells. 2005 Apr;23(4):544-9 PMID: 15790775
  22. Microarray results: how accurate are they?
    BMC Bioinformatics. 2002 Aug 23;3:22 PMID: 12194703
  23. Standardizing global gene expression analysis between laboratories and across platforms.
    Nat Methods. 2005 May;2(5):351-6 PMID: 15846362
  24. Analysis of matched mRNA measurements from two different microarray technologies.
    Bioinformatics. 2002 Mar;18(3):405-12 PMID: 11934739
  25. Genomic analysis of early murine mammary gland development using novel probe-level algorithms.
    Genome Biol. 2005;6(2):R20 PMID: 15693949
  26. Combining multiple microarray studies and modeling interstudy variation.
    Bioinformatics. 2003;19 Suppl 1:i84-90 PMID: 12855442
  27. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling.
    Cancer Cell. 2002 Mar;1(2):133-43 PMID: 12086872
  28. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D39-45 PMID: 15608222
  29. Evaluation of gene expression measurements from commercial microarray platforms.
    Nucleic Acids Res. 2003 Oct 1;31(19):5676-84 PMID: 14500831
  30. Independence and reproducibility across microarray platforms.
    Nat Methods. 2005 May;2(5):337-44 PMID: 15846360
  31. Multiple-laboratory comparison of microarray platforms.
    Nat Methods. 2005 May;2(5):345-50 PMID: 15846361
  32. Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
    Biostatistics. 2003 Apr;4(2):249-64 PMID: 12925520
  33. Leveraging two-way probe-level block design for identifying differential gene expression with high-density oligonucleotide arrays.
    BMC Bioinformatics. 2004 Apr 20;5:42 PMID: 15099405
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gni193
Email
[email protected]
Published
2005-12-14
Epub
2005-00-14
Pages
e193
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1316121
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gni193 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2