LPE
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see LPE.
Methods for analyzing microarray data using Local Pooled Error (LPE) method
Bioconductor version: 3.9
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("LPE")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Microarray, Software |
| Version | 1.58.0 |
| 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_1.58.0.tar.gz |
| Windows Binary | LPE_1.58.0.zip |
| Mac OS X 10.11 (El Capitan) | LPE_1.58.0.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 |
| Old Source Packages for BioC 3.9 | Source Archive |