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SCAN.UPC

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


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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")
Primer PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews ImmunoOncology, Microarray, OneChannel, Preprocessing, RNASeq, Software, TwoChannel
Version 2.44.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 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
System Requirements
URL http://bioconductor.org http://jlab.bu.edu/software/scan-upc
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Suggests pd.hg.u95a
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Package Archives

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

Source Package SCAN.UPC_2.44.0.tar.gz
Windows Binary SCAN.UPC_2.44.0.zip
macOS Binary (x86_64) SCAN.UPC_2.44.0.tgz
macOS Binary (arm64) SCAN.UPC_2.44.0.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/
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