To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("SCAN.UPC")

In most cases, you don't need to download the package archive at all.

SCAN.UPC

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

Bioconductor version: Release (2.14)

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 hsc.utah.edu>

To install this package, start R and enter:

Citation (from within R, enter citation("SCAN.UPC")):

Installation

source("http://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 2.6.3
In Bioconductor since BioC 2.11 (R-2.15)
License MIT
Depends R (>= 2.14.0), Biobase(>= 2.6.0), oligo, Biostrings, GEOquery, affy, affyio, foreach, sva
Imports utils, methods, MASS, tools
Suggests pd.hg.u95a
System Requirements
URL http://bioconductor.org http://jlab.bu.edu/software/scan-upc
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source SCAN.UPC_2.6.3.tar.gz
Windows Binary SCAN.UPC_2.6.3.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SCAN.UPC_2.6.3.tgz
Mac OS X 10.9 (Mavericks) SCAN.UPC_2.6.3.tgz
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