panp
Presence-Absence Calls from Negative Strand Matching Probesets
Bioconductor version: 2.9
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
| R Script | gene presence/absence calls | |
| Reference Manual |
Details
| biocViews | Infrastructure |
| Depends | R (>= 2.5.0), affy(>= 1.23.4), Biobase(>= 2.5.5) |
| Imports | Biobase, methods, stats, utils |
| Suggests | |
| System Requirements | |
| License | GPL (>= 2) |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Version | 1.24.0 |
| Since | Bioconductor 1.8 (R-2.3) |
Package Downloads
| Package Source | panp_1.24.0.tar.gz |
| Windows Binary | panp_1.24.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | panp_1.24.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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