Registration Open for Bioc2024 July 24-26


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 (3.20)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


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


To view documentation for the version of this package installed in your system, start R and enter:

Primer PDF R Script
Reference Manual PDF


biocViews ImmunoOncology, Microarray, OneChannel, Preprocessing, RNASeq, Software, TwoChannel
Version 2.47.0
In Bioconductor since BioC 2.11 (R-2.15) (12 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
See More
Suggests pd.hg.u95a
Linking To
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package SCAN.UPC_2.47.0.tar.gz
Windows Binary
macOS Binary (x86_64) SCAN.UPC_2.47.0.tgz
macOS Binary (arm64) SCAN.UPC_2.47.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats