Single-channel array normalization (SCAN) and University Probability of expression Codes (UPC)

Bioconductor version: Release (2.12)

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 Probability of expression Codes (UPC) method is an extension of SCAN that generates probability-of-expression values. These values can be interpreted as the probability that a given genomic feature (e.g., gene, transcript) is expressed above the background 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 W. Evan Johnson

Maintainer: Stephen R. Piccolo <stephen.piccolo at>

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PDF R Script SCAN - Primer
PDF   Reference Manual


biocViews Microarray, OneChannel, Preprocessing, RNAseq, Software, TwoChannel
Version 2.0.2
In Bioconductor since BioC 2.11 (R-2.16)
License MIT
Depends R (>= 2.14.0), Biobase(>= 2.6.0), oligo, Biostrings
Imports utils, methods, MASS, tools
Suggests pd.hg.u95a
System Requirements
Depends On Me
Imports Me
Suggests Me

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Package Source SCAN.UPC_2.0.2.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) SCAN.UPC_2.0.2.tgz
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