SCAN.UPC

DOI: 10.18129/B9.bioc.SCAN.UPC    

Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

Bioconductor version: Release (3.6)

SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.

Author: Stephen R. Piccolo and Andrea H. Bild and W. Evan Johnson

Maintainer: Stephen R. Piccolo <stephen_piccolo at byu.edu>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SCAN.UPC")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SCAN.UPC")

 

PDF	R Script	Primer
PDF		Reference Manual
Text		NEWS

Details

biocViews	Microarray, OneChannel, Preprocessing, RNASeq, Software, TwoChannel
Version	2.20.0
In Bioconductor since	BioC 2.11 (R-2.15) (5.5 years)
License	MIT
Depends	R (>= 2.14.0), Biobase(>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva
Imports	utils, methods, MASS, tools, IRanges
LinkingTo
Suggests	pd.hg.u95a
SystemRequirements
Enhances
URL	http://bioconductor.org http://jlab.bu.edu/software/scan-upc
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	SCAN.UPC_2.20.0.tar.gz
Windows Binary	SCAN.UPC_2.20.0.zip
Mac OS X 10.11 (El Capitan)	SCAN.UPC_2.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SCAN.UPC
Package Short Url	http://bioconductor.org/packages/SCAN.UPC/
Package Downloads Report	Download Stats