panp

Presence-Absence Calls from Negative Strand Matching Probesets

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("panp")

Documentation

PDF R Script gene presence/absence calls
PDF   Reference Manual

Details

biocViews Infrastructure, Software
Version 1.35.0
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
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Package Downloads

Package Source panp_1.35.0.tar.gz
Windows Binary panp_1.35.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) panp_1.35.0.tgz
Mac OS X 10.9 (Mavericks)
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