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snm

Supervised Normalization of Microarrays

Bioconductor version: Release (3.17)

SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.

Author: Brig Mecham and John D. Storey <jstorey at princeton.edu>

Maintainer: John D. Storey <jstorey at princeton.edu>

Citation (from within R, enter citation("snm")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("snm")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("snm")
snm Tutorial PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, ExonArray, GeneExpression, Microarray, MultiChannel, MultipleComparison, OneChannel, Preprocessing, QualityControl, Software, Transcription, TwoChannel
Version 1.48.0
In Bioconductor since BioC 2.8 (R-2.13) (12.5 years)
License LGPL
Depends R (>= 2.12.0)
Imports corpcor, lme4 (>= 1.0), splines
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Depends On Me
Imports Me edge, ExpressionNormalizationWorkflow
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package snm_1.48.0.tar.gz
Windows Binary snm_1.48.0.zip
macOS Binary (x86_64) snm_1.48.0.tgz
macOS Binary (arm64) snm_1.48.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/snm
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/snm
Bioc Package Browser https://code.bioconductor.org/browse/snm/
Package Short Url https://bioconductor.org/packages/snm/
Package Downloads Report Download Stats