To install this package, start R and enter:

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

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

panp

Presence-Absence Calls from Negative Strand Matching Probesets

Bioconductor version: Release (2.14)

A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

Author: Peter Warren

Maintainer: Peter Warren <peter.warren at verizon.net>

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("panp")

 

PDF R Script gene presence/absence calls
PDF   Reference Manual

Details

biocViews Infrastructure, Software
Version 1.34.0
In Bioconductor since BioC 1.8 (R-2.3)
License GPL (>= 2)
Depends R (>= 2.10), affy(>= 1.23.4), Biobase(>= 2.5.5)
Imports Biobase, methods, stats, utils
Suggests gcrma
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source panp_1.34.0.tar.gz
Windows Binary panp_1.34.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) panp_1.34.0.tgz
Mac OS X 10.9 (Mavericks) panp_1.34.0.tgz
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