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: 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")
| R Script | LPE test for microarray data with small number of replicates | |
| 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 |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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