ReviewBriefings in bioinformatics2010
Detection call algorithms for high-throughput gene expression microarray data.
Review in Briefings in bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Unveiling Prognostic RNA Biomarkers through a Multi-Cohort Study in Colorectal Cancer.International journal of molecular sciences · 2024Article
- Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition.Scientific reports · 2019Article
- Review and Meta-Analyses of TAAR1 Expression in the Immune System and Cancers.Frontiers in pharmacology · 2018Article
- Aberrant activation of the human sex-determining gene in early embryonic development results in postnatal growth retardation and lethality in mice.Scientific reports · 2017Article
- Unique intrahepatic transcriptomics profiles discriminate the clinical phases of a chronic HBV infection.PloS one · 2017Article
- HDAC6 Deacetylates HMGN2 to Regulate Stat5a Activity and Breast Cancer Growth.Molecular cancer research : MCR · 2016Article
- Comparison of pre-processing methods for multiplex bead-based immunoassays.BMC genomics · 2016Article
- Systematic identification of 3'-UTR regulatory elements in activity-dependent mRNA stability in hippocampal neurons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2014Article
- Eureka-DMA: an easy-to-operate graphical user interface for fast comprehensive investigation and analysis of DNA microarray data.BMC bioinformatics · 2014Article
- Rab5 and Rab4 regulate axon elongation in the Xenopus visual system.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2014Article
- Genome wide analysis of sex difference in gene expression profiles of bone formations using sfx mice and BXD RI strains.TheScientificWorldJournal · 2014Article
- Exposure to cobalt causes transcriptomic and proteomic changes in two rat liver derived cell lines.PloS one · 2013Article
- Identification of biomarkers to assess organ quality and predict posttransplantation outcomes.Transplantation · 2012Article
- Detection of expression quantitative trait Loci in complex mouse crosses: impact and alleviation of data quality and complex population substructure.Frontiers in genetics · 2012Article
- Article
- Exposure to nickel, chromium, or cadmium causes distinct changes in the gene expression patterns of a rat liver derived cell line.PloS one · 2011Article
- Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips.Nucleic acids research · 2010Article
- Genetic diversity and striatal gene networks: focus on the heterogeneous stock-collaborative cross (HS-CC) mouse.BMC genomics · 2010Article
- Estimating the proportion of microarray probes expressed in an RNA sample.Nucleic acids research · 2010Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Extensive methodological research has been conducted to improve gene expression summary methods. However, in addition to quantitative gene expression summaries, most platforms, including all those examined in the MicroArray Quality Control project, provide a qualitative detection call result for each gene on the platform. These detection call algorithms are intended to render an assessment of whether or not each transcript is reliably measured. In this paper, we review uses of these qualitative detection call results in the analysis of microarray data. We also review the detection call algorithms for two widely used gene expression microarray platforms, Affymetrix GeneChips and Illumina BeadArrays, and more clearly formalize the mathematical notation for the Illumina BeadArray detection call algorithm. Both algorithms result in a P-value which is then used for determining the qualitative detection calls. We examined the performance of these detection call algorithms and default parameters by applying the methods to two spike-in datasets. We show that the default parameters for qualitative detection calls yield few absent calls for high spike-in concentrations. When genes of interest are expected to be present at very low concentrations, spike-in datasets can be useful for appropriately adjusting the tuning parameters for qualitative detection calls.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.