SCAN.UPC

Package: SCAN.UPC
Type: Package
Title: Single-channel array normalization (SCAN) and Universal
exPression Codes (UPC)
Version: 2.14.0
Author: Stephen R. Piccolo and Andrea H. Bild and W. Evan Johnson
Maintainer: Stephen R. Piccolo <stephen_piccolo@byu.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 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.
License: MIT
Depends: R (>= 2.14.0), Biobase (>= 2.6.0), oligo, Biostrings,
GEOquery, affy, affyio, foreach, sva
Suggests: pd.hg.u95a
Imports: utils, methods, MASS, tools, IRanges
URL: http://bioconductor.org, http://jlab.bu.edu/software/scan-upc
biocViews: Software, Microarray, Preprocessing, RNASeq, TwoChannel,
OneChannel
NeedsCompilation: no
Packaged: 2016-05-04 04:44:11 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SCAN.UPC' ...
** R
** inst
** preparing package for lazy loading
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
** help
*** installing help indices
  converting help for package 'SCAN.UPC'
    finding HTML links ... done
    BatchAdjust                             html  
    BatchAdjustFromFile                     html  
    InstallBrainArrayPackage                html  
    ParseMetaFromGtfFile                    html  
    SCAN                                    html  
    SCAN_TwoColor                           html  
    UPC_Generic                             html  
    UPC_Generic_ExpressionSet               html  
    UPC_RNASeq                              html  
    UPC_RNASeq_Single                       html  
    UPC_TwoColor                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Parallel computing support for 'oligo/crlmm': Disabled
     - Load 'ff'
     - Load and register a 'foreach' adaptor
        Example - Using 'multicore' for 2 cores:
             library(doMC)
             registerDoMC(2)
================================================================================
* DONE (SCAN.UPC)
Making 'packages.html' ... done