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nondetects specifications


Unique identifier OMICS_03938
Name nondetects
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.10.0
Stability Stable
limma, methods, utils, RUnit, rmarkdown, knitr, BiocGenerics(>=0.8.0), mvtnorm, R(>=3.2), Biobase(>=2.22.0), arm, HTqPCR(>=1.16.0), BiocStyle(>=1.0.0)
Maintained Yes


No version available



  • person_outline Matthew McCall

Publication for nondetects


On non-detects in qPCR data.

2014 Bioinformatics
PMCID: 4133581
PMID: 24764462
DOI: 10.1093/bioinformatics/btu239

nondetects citations


A novel two score system for interferon status segregates autoimmune diseases and correlates with clinical features

Sci Rep
PMCID: 5895784
PMID: 29643425
DOI: 10.1038/s41598-018-24198-1

[…] variables. fa included expression levels for isgs measured in the pmbcs from sle, uctd, ra and hc., prior to factor analysis (fa), undetected ∆ct values were singly imputed using the r package nondetects. the kaiser-meyer-olkin measure was used to verify the sampling adequacy of the analysis. principal factor extraction, without rotation, was used to identify the optimum number of factors, […]


Promising Prebiotic Candidate Established by Evaluation of Lactitol, Lactulose, Raffinose, and Oligofructose for Maintenance of a Lactobacillus Dominated Vaginal Microbiota

Appl Environ Microbiol
PMCID: 5812932
PMID: 29269494
DOI: 10.1128/AEM.02200-17

[…] by the nanodrop nd-1000 spectrophotometer (nanodrop technologies, inc., wilmington, de) and known gene copies per genome were determined by searching the organism in the ncbi genome database. nondetects were treated as containing no dna and averaged with concentrations of other replicates to reduce positive bias ()., to precipitate proteins, 100 μl of supernatant from swabs grown […]


Impact of an historic underground gas well blowout on the current methane chemistry in a shallow groundwater system

Proc Natl Acad Sci U S A
PMCID: 5777038
PMID: 29279383
DOI: 10.1073/pnas.1711472115

[…] monitoring for gas contamination should be conducted in close proximity to potential gas leakage sources, and at multiple monitoring locations. relying on single sampling points may lead to false “nondetects” if the monitoring distance is too large. in addition, the compositional and isotopic impact of oxidation may lead to erroneous assessment of the origin of dissolved gases, especially […]


Quantitative Microbial Risk Assessment for Spray Irrigation of Dairy Manure Based on an Empirical Fate and Transport Model

Environ Health Perspect
PMCID: 5884668
PMID: 28885976
DOI: 10.1289/EHP283

[…] used probit models to estimate the probability of detection and linear models to estimate concentration conditional on a detectable value (). this approach alleviated the need to impute values for nondetects prior to model fitting while simultaneously allowing the use of the full data set for each response variable. in the qmra (see below), we used the probit model to predict the distribution […]


Signs of innate immune activation and premature immunosenescence in psoriasis patients

Sci Rep
PMCID: 5548718
PMID: 28790368
DOI: 10.1038/s41598-017-07975-2

[…] fail to reach the prespecified minimum signal intensity threshold (i.e 40 cycles), , they were imputed using expectation-maximization algorithm described in mccall et al., implemented in r package nondetects ver. 2.2.0 available from bioconductor., in order to ensure expression stability of the reference gene, its ct values were filtered based on interquartile range (iqr). observations […]


Comparison of soil sampling and analytical methods for asbestos at the Sumas Mountain Asbestos Site—Working towards a toolbox for better assessment

PLoS One
PMCID: 5536314
PMID: 28759607
DOI: 10.1371/journal.pone.0180210

[…] error was responsible for elevated rsds as laboratory replicates showed good agreement. the data for other analytical methods did not lend itself to this approach due to the high frequency of nondetects in the asbestos data set., this project supports the need for better, more accurate methods for determining asbestos levels in soils. variability occurs during sample collection […]

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nondetects institution(s)
University of Rochester Medical Center, Rochester, NY, USA; University of Rochester, Rochester, NY, USA

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