LPE

DOI: 10.18129/B9.bioc.LPE  

Methods for analyzing microarray data using Local Pooled Error (LPE) method

Bioconductor version: Release (3.16)

This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.

Author: Nitin Jain <emailnitinjain at gmail.com>, Michael O'Connell <michaelo at warath.com>, Jae K. Lee <jaeklee at virginia.edu>. Includes R source code contributed by HyungJun Cho <hcho at virginia.edu>

Maintainer: Nitin Jain <emailnitinjain at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("LPE")

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("LPE")

 

PDF	R Script	LPE test for microarray data with small number of replicates
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, Microarray, Software
Version	1.72.0
In Bioconductor since	BioC 1.6 (R-2.1) or earlier (> 18 years)
License	LGPL
Depends	R (>= 2.10)
Imports	stats
LinkingTo
Suggests
SystemRequirements
Enhances
URL	http://www.r-project.org http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ http://sourceforge.net/projects/r-lpe/
Depends On Me	LPEadj, PLPE
Imports Me	LPEadj
Suggests Me	ABarray
Links To Me
Build Report

Package Archives

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

Source Package	LPE_1.72.0.tar.gz
Windows Binary	LPE_1.72.0.zip
macOS Binary (x86_64)	LPE_1.72.0.tgz
macOS Binary (arm64)	LPE_1.72.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/LPE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/LPE
Bioc Package Browser	https://code.bioconductor.org/browse/LPE/
Package Short Url	https://bioconductor.org/packages/LPE/
Package Downloads Report	Download Stats