ArticleBMC genomics2007
Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers, 1 of them a synthesis that pooled it.
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Who cites it
33 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A cross-laboratory comparison of expression profiling data from normal human postmortem brain.Neuroscience · 2010Pooled it
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- Post genome-wide association analysis: dissecting computational pathway/network-based approaches.Briefings in bioinformatics · 2019Review
- OPATs: Omnibus P-value association tests.Briefings in bioinformatics · 2019Review
- rPCMP: robust p-value combination by multiple partitions with applications to ATAC-seq data.BMC systems biology · 2018Article
- Gene-level differential analysis at transcript-level resolution.Genome biology · 2018Article
- Discovery of new candidate genes for rheumatoid arthritis through integration of genetic association data with expression pathway analysis.Arthritis research & therapy · 2017Article
- Group-combined P-values with applications to genetic association studies.Bioinformatics (Oxford, England) · 2016Article
- Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.Molecular systems biology · 2014Article
- Mucosal transcriptomics implicates under expression of BRINP3 in the pathogenesis of ulcerative colitis.Inflammatory bowel diseases · 2014Article
- Fisher's method of combining dependent statistics using generalizations of the gamma distribution with applications to genetic pleiotropic associations.Biostatistics (Oxford, England) · 2014Article
- A Comparison of Combined P-value Methods for Gene Differential Expression Using RNA-Seq Data.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2014Article
- An Island-Based Approach for Differential Expression Analysis.2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics : ACM - BCB 2013 : Washington, D.C., U.S.A., September 22 - 25, 2013. ACM Conference on Bioinformatics, Computational Biology and Biomedical Informa... · 2013Article
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- Genome-wide survey of cold stress regulated alternative splicing in Arabidopsis thaliana with tiling microarray.PloS one · 2013Article
- Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways.PloS one · 2012Article
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- Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy.PloS one · 2011Article
- A genome-wide SNP scan reveals novel loci for egg production and quality traits in white leghorn and brown-egg dwarf layers.PloS one · 2011Article
Corrections and comments
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2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrently, most tests of differential gene expression using Affymetrix expression array data are performed using expression summary values representing each probe set on a microarray. Recently testing methods have been proposed which incorporate probe level information. We propose a new approach that uses Fisher's method of combining evidence from multiple sources of information. Specifically, we combine p-values from probe level tests of significance.
resultsThe combined p method and other competing methods were compared using three spike-in datasets (where probe sets corresponding differentially spiked transcripts are known) and array data from a biological study validated with qRT-PCR. Based on power and false discovery rates computed for the spike-in datasets, we demonstrate that the combined p method compares favorably with other methods. We find that probe level testing methods select many of the same genes as differentially expressed. We illustrate the use of the combined p method for diagnostic purposes using examples.
conclusionCombined p is a promising alternative to existing methods of testing for differential gene expression. In addition, the combined p method is particularly well suited as a diagnostic tool for exploratory analysis of microarray data.
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