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

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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
Date of publication
None
Maintainer
Stephen R. Piccolo <stephen_piccolo@byu.edu>
License
MIT
Version
2.16.0
URLs

View on Bioconductor

Man pages

BatchAdjust
Helper function for applying the ComBat batch-adjusting...
BatchAdjustFromFile
Helper function for applying the ComBat batch-adjusting...
InstallBrainArrayPackage
Helper function for installing BrainArray packages
ParseMetaFromGtfFile
Helper function to parse length and GC content information...
SCAN
Single-Channel Array Normalization (SCAN) and Universal...
SCAN_TwoColor
Single-Channel Array Normalization (SCAN) for Agilent...
UPC_Generic
Generic function to apply Universal exPression Codes (UPC)...
UPC_Generic_ExpressionSet
Generic function to apply Universal exPression Codes (UPC)...
UPC_RNASeq
Universal exPression Codes (UPC) for RNA-Seq data
UPC_RNASeq_Single
Apply Universal exPression Codes (UPC) transformation to a...
UPC_TwoColor
Universal exPression Codes (UPC) for two-channel microarrays

Files in this package

SCAN.UPC/DESCRIPTION
SCAN.UPC/NAMESPACE
SCAN.UPC/NEWS
SCAN.UPC/R
SCAN.UPC/R/Helper.R
SCAN.UPC/R/OneColor.R
SCAN.UPC/R/RNASeq.R
SCAN.UPC/R/TwoColor.R
SCAN.UPC/R/UPC_Models.R
SCAN.UPC/R/channelNormalize.R
SCAN.UPC/R/iglNormalize.R
SCAN.UPC/R/madNormalize.R
SCAN.UPC/R/normalizeArray.R
SCAN.UPC/R/quantileNormalize.R
SCAN.UPC/R/readAgilentData.R
SCAN.UPC/build
SCAN.UPC/build/vignette.rds
SCAN.UPC/inst
SCAN.UPC/inst/CITATION
SCAN.UPC/inst/doc
SCAN.UPC/inst/doc/SCAN.vignette.R
SCAN.UPC/inst/doc/SCAN.vignette.Rnw
SCAN.UPC/inst/doc/SCAN.vignette.pdf
SCAN.UPC/man
SCAN.UPC/man/BatchAdjust.Rd
SCAN.UPC/man/BatchAdjustFromFile.Rd
SCAN.UPC/man/InstallBrainArrayPackage.Rd
SCAN.UPC/man/ParseMetaFromGtfFile.Rd
SCAN.UPC/man/SCAN.Rd
SCAN.UPC/man/SCAN_TwoColor.Rd
SCAN.UPC/man/UPC_Generic.Rd
SCAN.UPC/man/UPC_Generic_ExpressionSet.Rd
SCAN.UPC/man/UPC_RNASeq.Rd
SCAN.UPC/man/UPC_RNASeq_Single.Rd
SCAN.UPC/man/UPC_TwoColor.Rd
SCAN.UPC/svnignore.txt
SCAN.UPC/vignettes
SCAN.UPC/vignettes/BrainArray.png
SCAN.UPC/vignettes/SCAN.vignette.Rnw
SCAN.UPC/vignettes/SCAN.vignette.bib