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.

Author
Peter Warren
Date of publication
None
Maintainer
Peter Warren <peter.warren@verizon.net>
License
GPL (>= 2)
Version
1.44.0

View on Bioconductor

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...

Files in this package

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