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LPE

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
LPE test for microarray data with small number of replicates PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, Microarray, Software
Version 1.76.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License LGPL
Depends R (>= 2.10)
Imports stats
System Requirements
URL http://www.r-project.org http://www.healthsystem.virginia.edu/internet/hes/biostat/bioinformatics/ http://sourceforge.net/projects/r-lpe/
See More
Suggests
Linking To
Enhances
Depends On Me LPEadj, PLPE
Imports Me LPEadj
Suggests Me ABarray
Links To Me
Build Report Build Report

Package Archives

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

Source Package LPE_1.76.0.tar.gz
Windows Binary LPE_1.76.0.zip
macOS Binary (x86_64) LPE_1.76.0.tgz
macOS Binary (arm64) LPE_1.76.0.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