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nondetects specifications

Information


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
Requirements
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

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Documentation


Maintainer


  • person_outline Matthew McCall <>

Publications for nondetects

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On non-detects in qPCR data.

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

nondetects in publications

 (53)
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, […]

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 […]

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 […]

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 […]

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 […]


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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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