To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("panp")

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

panp

   

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see panp.

Presence-Absence Calls from Negative Strand Matching Probesets

Bioconductor version: 3.2

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:

## try http:// if https:// URLs are not supported
source("https://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 gene presence/absence calls
PDF   Reference Manual

Details

biocViews Infrastructure, Software
Version 1.40.0
In Bioconductor since BioC 1.8 (R-2.3) (10 years)
License GPL (>= 2)
Depends R (>= 2.10), affy(>= 1.23.4), Biobase(>= 2.5.5)
Imports Biobase, methods, stats, utils
LinkingTo
Suggests gcrma
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source panp_1.40.0.tar.gz
Windows Binary panp_1.40.0.zip
Mac OS X 10.6 (Snow Leopard) panp_1.40.0.tgz
Mac OS X 10.9 (Mavericks) panp_1.40.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/panp/tree/release-3.2
Package Short Url http://bioconductor.org/packages/panp/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center