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>

To install this package, start R and enter:

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

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

Documentation

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 Downloads

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
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