Bioconductor-mirror/SCAN.UPC: Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)

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.

Getting started

Package details

AuthorStephen R. Piccolo and Andrea H. Bild and W. Evan Johnson
Bioconductor views Microarray OneChannel Preprocessing RNASeq Software TwoChannel
MaintainerStephen R. Piccolo <[email protected]>
Package repositoryView on GitHub
Installation Install the latest version of this package by entering the following in R:
Bioconductor-mirror/SCAN.UPC documentation built on June 1, 2017, 1:13 a.m.