panp: Presence-Absence Calls from Negative Strand Matching Probesets
Version 1.46.0

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.

AuthorPeter Warren
Bioconductor views Infrastructure
Date of publicationNone
MaintainerPeter Warren <peter.warren@verizon.net>
LicenseGPL (>= 2)
Version1.46.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("panp")

Popular man pages

gcrma.ExpressionSet: ExpressionSet resulting from gcrma processing of 3 HG-U133A...
NSMPnames.hgu133a: Negative Strand Matching Probeset (NSMP) names for HG-U133A...
NSMPnames.hgu133plus2: Negative Strand Matching Probeset (NSMP) names for HG-U133...
pa.calls: Presence-Absence Calls from Negative Strand Matching...
See all...

All man pages Function index File listing

Man pages

gcrma.ExpressionSet: ExpressionSet resulting from gcrma processing of 3 HG-U133A...
NSMPnames.hgu133a: Negative Strand Matching Probeset (NSMP) names for HG-U133A...
NSMPnames.hgu133plus2: Negative Strand Matching Probeset (NSMP) names for HG-U133...
pa.calls: Presence-Absence Calls from Negative Strand Matching...

Functions

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
panp documentation built on May 20, 2017, 10:17 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.