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 (3.22)
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, entercitation("SCAN.UPC")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SCAN.UPC")Follow Installation instructions to use this package in your R session.
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