panp: Presence-Absence Calls from Negative Strand Matching Probesets

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("panp")
AuthorPeter Warren
Bioconductor views Infrastructure
Date of publicationNone
MaintainerPeter Warren <peter.warren@verizon.net>
LicenseGPL (>= 2)
Version1.44.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/pa.calls.R
build
build/vignette.rds
data
data/NSMPnames.hgu133a.rda
data/NSMPnames.hgu133plus2.rda
data/gcrma.ExpressionSet.rda
inst
inst/doc
inst/doc/panp.R
inst/doc/panp.Rnw
inst/doc/panp.pdf
man
man/NSMPnames.hgu133a.Rd man/NSMPnames.hgu133plus2.Rd man/gcrma.ExpressionSet.Rd man/pa.calls.Rd
vignettes
vignettes/panp.Rnw

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