SCAN.UPC

DOI: 10.18129/B9.bioc.SCAN.UPC  

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

Bioconductor version: Release (3.16)

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 (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SCAN.UPC")

For older versions of R, please refer to the appropriate Bioconductor release.

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	ImmunoOncology, Microarray, OneChannel, Preprocessing, RNASeq, Software, TwoChannel
Version	2.40.0
In Bioconductor since	BioC 2.11 (R-2.15) (10.5 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
Links To Me
Build Report

Package Archives

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

Source Package	SCAN.UPC_2.40.0.tar.gz
Windows Binary	SCAN.UPC_2.40.0.zip
macOS Binary (x86_64)	SCAN.UPC_2.40.0.tgz
macOS Binary (arm64)	SCAN.UPC_2.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/SCAN.UPC
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/SCAN.UPC
Bioc Package Browser	https://code.bioconductor.org/browse/SCAN.UPC/
Package Short Url	https://bioconductor.org/packages/SCAN.UPC/
Package Downloads Report	Download Stats