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

panp

Presence-Absence Calls from Negative Strand Matching Probesets

Bioconductor version: 2.13

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>

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	1.32.0
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
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Package Archives

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

Package Source	panp_1.32.0.tar.gz
Windows Binary	panp_1.32.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	panp_1.32.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats