Package: SCAN.UPC
Type: Package
Title: Single-channel array normalization (SCAN) and Universal
        exPression Codes (UPC)
Version: 2.4.2
Author: Stephen R. Piccolo and Andrea H. Bild and W. Evan Johnson
Maintainer: Stephen R. Piccolo <stephen.piccolo@hsc.utah.edu>
Description: 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 estimate 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.)
License: MIT
Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
        GEOquery, affy, affyio, foreach
Suggests: pd.hg.u95a
Imports: utils, methods, MASS, tools
biocViews: Software, Microarray, Preprocessing, RNAseq, TwoChannel,
        OneChannel
URL: http://bioconductor.org, http://jlab.bu.edu/software/scan-upc
Packaged: 2014-03-29 08:25:53 UTC; biocbuild
Built: R 3.0.3; ; 2014-03-29 13:44:06 UTC; windows
