To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("LPE")

In most cases, you don't need to download the package archive at all.

LPE

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

Bioconductor version: Release (2.14)

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 and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("LPE")

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 1.38.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License LGPL
Depends R (>= 2.10)
Imports stats
Suggests
System Requirements
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

Package Archives

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

Package Source LPE_1.38.0.tar.gz
Windows Binary LPE_1.38.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) LPE_1.38.0.tgz
Mac OS X 10.9 (Mavericks) LPE_1.38.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center