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Protocols

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

Versioning


No version available

Documentation


Maintainer


  • person_outline Matthew McCall

Publication for nondetects

library_books

On non-detects in qPCR data

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

nondetects citations

 (4)
library_books

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

2018
Sci Rep
PMCID: 5895784
PMID: 29643425
DOI: 10.1038/s41598-018-24198-1

[…] ntinuous 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, […]

call_split

Replication Study: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

2018
eLife
PMCID: 5849410
PMID: 29533182
DOI: 10.7554/eLife.25801.012
call_split See protocol

[…] e8q/. For all qPCR runs, the F. nucleatum assay had a baseline of cycles 3–30 and a threshold of 0.2 and the PGT assay had a baseline of cycles 3–20 and a threshold of 0.1. For qPCR preprocessing all nondetects were set to 40. Technical duplicates were averaged for each sample. Fold difference in F. nucleatum abundance in tumor versus normal tissue was determined using the ∆∆Ct method (). For each […]

library_books

Signs of innate immune activation and premature immunosenescence in psoriasis patients

2017
Sci Rep
PMCID: 5548718
PMID: 28790368
DOI: 10.1038/s41598-017-07975-2

[…] e. 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. […]

library_books

A four gene signature predictive of recurrent prostate cancer

2016
Oncotarget
PMCID: 5356893
PMID: 27966447
DOI: 10.18632/oncotarget.13837

[…] Ct values were normalized to Becn1. Non-detects were imputed based on estimation of a non-random missing data mechanism using the nondetects R/Bioconductor package.18 Statistical assessment of differential expression was performed using a t-test based on maximum likelihood estimates (MLEs) of the within group means and variances […]

Citations

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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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