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panp (version 1.42.0)

Presence-Absence Calls from Negative Strand Matching Probesets

Description

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.

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Version

Version

1.42.0

License

GPL (>= 2)

Maintainer

Peter Warren

Last Published

February 15th, 2017

Functions in panp (1.42.0)

gcrma.ExpressionSet

ExpressionSet resulting from gcrma processing of 3 HG-U133A chips
pa.calls

Presence-Absence Calls from Negative Strand Matching Probesets
NSMPnames.hgu133a

Negative Strand Matching Probeset (NSMP) names for HG-U133A chip type
NSMPnames.hgu133plus2

Negative Strand Matching Probeset (NSMP) names for HG-U133 Plus 2.0 chip type