ArticleBioinformatics (Oxford, England)2014
On non-detects in qPCR data.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 102 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
102 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Replication Study:eLife · 2018Pooled it
- Infant circulating MicroRNAs as biomarkers of effect in fetal alcohol spectrum disorders.Scientific reports · 2021Trial
- Investigating circadian clock gene expression in human tendon biopsies from acute exercise and immobilization studies.European journal of applied physiology · 2019Trial
- Trial
- Accounting for methodological variabilities in disease outbreak surveillance using wastewater-based epidemiology: a case study with SARS-CoV-2.Analytical and bioanalytical chemistry · 2026Article
- Accounting for temporal variation and correlation in environmental DNA sampling can improve ecological inferences.Ecological applications : a publication of the Ecological Society of America · 2026Article
- Time-dependent changes in monocyte subsets and gene expression patterns are associated with long-term recovery in patients with ischemic stroke.Research square · 2026Article
- First molecular confirmations of Anopheles dirus and Anopheles scanloni in Indonesia, with DNA of zoonotic, enzootic and human malarias detected in An. dirus.Scientific reports · 2026Article
- MicroRNA Profiling as a Novel Predictive Tool for Operational Tolerance in Pediatric Liver Transplantation: A Single-center Study.Transplantation direct · 2026Article
- Evidence incriminating Anopheles maculatus as a potential vector of Plasmodium knowlesi and Plasmodium inui.Scientific reports · 2026Article
- Article
- The longitudinal expression ofMicrobiology (Reading, England) · 2026Article
- Test, Treat, Repopulate™ method reduces red complex bacteria and stabilizes the oral microbiome.Frontiers in dental medicine · 2026Article
- Development of a TK6-derived cell line expressing four human cytochrome P450s for genotoxicity testing.Toxicology in vitro : an international journal published in association with BIBRA · 2025Article
- Review
- Development of a New Trapping System with Potential Implementation as a Tool for Mosquito-Borne Arbovirus Surveillance.Insects · 2025Article
- Evaluating the factors influencing accuracy, interpretability, and reproducibility in the use of machine learning classifiers in biology to enable standardization.Scientific reports · 2025Article
- NLRP3 is a BMI-independent mediator of stable COPD.BMC pulmonary medicine · 2025Article
- A simplified MyProstateScore2.0 for high-grade prostate cancer.Cancer biomarkers : section A of Disease markers · 2025Article
- Article
42 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
motivationQuantitative real-time PCR (qPCR) is one of the most widely used methods to measure gene expression. Despite extensive research in qPCR laboratory protocols, normalization and statistical analysis, little attention has been given to qPCR non-detects-those reactions failing to produce a minimum amount of signal.
resultsWe show that the common methods of handling qPCR non-detects lead to biased inference. Furthermore, we show that non-detects do not represent data missing completely at random and likely represent missing data occurring not at random. We propose a model of the missing data mechanism and develop a method to directly model non-detects as missing data. Finally, we show that our approach results in a sizeable reduction in bias when estimating both absolute and differential gene expression. AVAILABILITY AND IMPLEMENTATION: The proposed algorithm is implemented in the R package, nondetects. This package also contains the raw data for the three example datasets used in this manuscript. The package is freely available at http://mnmccall.com/software and as part of the Bioconductor project.
Indexed as
Identifiers
What OpenQuestion holds
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.