This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

SCAN.UPC

This is the development version of SCAN.UPC; for the stable release version, see SCAN.UPC.

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

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.43.0
In Bioconductor since BioC 2.11 (R-2.15) (11 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
Linking To
Suggests pd.hg.u95a
System Requirements
Enhances
URL http://bioconductor.org http://jlab.bu.edu/software/scan-upc
See More
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_2.43.0.tar.gz
Windows Binary SCAN.UPC_2.43.0.zip (64-bit only)
macOS Binary (x86_64) SCAN.UPC_2.43.0.tgz
macOS Binary (arm64) SCAN.UPC_2.43.0.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