ArticleNucleic acids research2005
Integrating probe-level expression changes across generations of Affymetrix arrays.
Article in Nucleic acids research, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- Semantic Signature: Comparative Interpretation of Gene Expression on a Semantic Space.Computational and mathematical methods in medicine · 2016Article
- A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.PloS one · 2014Article
- A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases.Nucleic acids research · 2013Article
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- Microarray Я US: a user-friendly graphical interface to Bioconductor tools that enables accurate microarray data analysis and expedites comprehensive functional analysis of microarray results.BMC research notes · 2012Article
- Integrative computational biology for cancer research.Human genetics · 2011Review
- GTI: a novel algorithm for identifying outlier gene expression profiles from integrated microarray datasets.PloS one · 2011Article
- Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome.PloS one · 2010Article
- Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation.Molecular & cellular proteomics : MCP · 2010Article
- Microarray probes and probe sets.Frontiers in bioscience (Elite edition) · 2010Review
- Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis.BMC proceedings · 2009Article
- Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees.BMC bioinformatics · 2009Article
- Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations.BMC bioinformatics · 2009Article
- Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies.Genome biology · 2009Article
- Key issues in conducting a meta-analysis of gene expression microarray datasets.PLoS medicine · 2008Review
- Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis.PloS one · 2008Article
- Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues.Genome biology · 2008Article
- Measuring global gene expression in polyploidy; a cautionary note from allohexaploid wheat.Functional & integrative genomics · 2007Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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