LPE

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

Bioconductor version: Development (2.8)

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, Michael O'Connell , Jae K. Lee . Includes R source code contributed by HyungJun Cho

Maintainer: Nitin Jain

To install this package, start R and enter:

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

Documentation

PDF

R Script

LPE test for microarray data with small number of replicates

Reference Manual

Details

biocViews	Microarray, Bioinformatics, DifferentialExpression
Depends
Imports	stats
Suggests
System Requirements
License	LGPL
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
Version	1.25.0

Package Downloads

Package Source	LPE_1.25.0.tar.gz
Windows Binary	LPE_1.25.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	LPE_1.25.0.tgz
Package Downloads Report	Download Stats