Package: plgem 1.85.0

Norman Pavelka

plgem: Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)

The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

Authors:Mattia Pelizzola <[email protected]> and Norman Pavelka <[email protected]>

plgem_1.85.0.tar.gz
plgem_1.85.0.zip(r-4.7)plgem_1.85.0.zip(r-4.6)plgem_1.85.0.zip(r-4.5)
plgem_1.85.0.tgz(r-4.6-any)plgem_1.85.0.tgz(r-4.5-any)
plgem_1.85.0.tar.gz(r-4.7-any)plgem_1.85.0.tar.gz(r-4.6-any)
plgem_1.85.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
plgem/json (API)

# Install 'plgem' in R:

install.packages('plgem', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

LPSeset - ExpressionSet for Testing PLGEM

On BioConductor:plgem-1.85.0(bioc 3.24)plgem-1.84.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology microarray differentialexpression proteomics geneexpression massspectrometry

4.38 score 1 packages 10 scripts 612 downloads 4 mentions 8 exports 4 dependencies

Last updated from:01627314fc. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	143
linux-devel-x86_64	OK	173
source / vignettes	OK	226
linux-release-x86_64	OK	254
macos-release-arm64	OK	86
macos-oldrel-arm64	OK	71
windows-devel	OK	103
windows-release	OK	83
windows-oldrel	OK	89
wasm-release	OK	97

Exports:plgem.deg plgem.fit plgem.obsStn plgem.pValue plgem.resampledStn plgem.write.summary run.plgem setGpar

Dependencies:Biobase BiocGenerics generics MASS

An introduction to PLGEM

Rendered fromplgem.Rnwusingutils::Sweave

Last update: 2013-02-06
Started: 2013-02-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ExpressionSet for Testing PLGEM	LPSeset
Selection of Differentially Expressed Genes/Proteins With PLGEM	plgem.deg
PLGEM Fitting and Evaluation	plgem.fit
Computation of Observed PLGEM-STN Statistics	plgem.obsStn
Computation of PLGEM p-values	plgem.pValue
Computation of Resampled PLGEM-STN Statistics	plgem.resampledStn
Write the Result of a PLGEM Analysis to the Working Directory	plgem.write.summary
Wrapper for Power Law Global Error Model (PLGEM) analysis method	run.plgem
Set graphical parameters for PLGEM fitting evaluation plots	setGpar