farms: FARMS - Factor Analysis for Robust Microarray Summarization
Version 1.28.0

The package provides the summarization algorithm called Factor Analysis for Robust Microarray Summarization (FARMS) and a novel unsupervised feature selection criterion called "I/NI-calls"

Browse man pages Browse package API and functions Browse package files

AuthorDjork-Arne Clevert <okko@clevert.de>
Bioconductor views GeneExpression Microarray Preprocessing QualityControl
Date of publicationNone
MaintainerDjork-Arne Clevert <okko@clevert.de>
LicenseLGPL (>= 2.1)
Version1.28.0
URL http://www.bioinf.jku.at/software/farms/farms.html
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("farms")

Man pages

dummy: Example cdfenv
expFarms: Factor Analysis for Robust Microarray Summarization
generateExprVal.method.farms: Generate an expression value from the probes informations
getI_Eset-methods: Method to generate an ExpressionSet of informative genes
getI_ProbeSets-methods: Method to generate a vector of informative probe set names
getNI_Eset-methods: Method to generate an ExpressionSet of non-informative genes
getNI_ProbeSets-methods: Method to generate a vector of non-informative probe set...
INI_Calls-class: Class INI_Calls
INIcalls-methods: Dimension reduction based on informative genes
lFarms: lFarms expression measure
plot-methods: Visualizes the distribution of informative and...
qFarms: qFarms expression measure
summary-methods: Summary of I/NI-calls
testAffyBatch: AffyBatch instance testAffyBatch

Functions

INI_Calls Man page
INI_Calls-class Man page
INIcalls Man page
INIcalls,ExpressionSet-method Man page
INIcalls-methods Man page
dummy Man page
expFarms Man page Source code
generateExprVal.method.farms Man page Source code
getI_Eset Man page
getI_Eset,INI_Calls-method Man page
getI_Eset-methods Man page
getI_ProbeSets Man page
getI_ProbeSets,INI_Calls-method Man page
getI_ProbeSets-methods Man page
getNI_Eset Man page
getNI_Eset,INI_Calls-method Man page
getNI_Eset-methods Man page
getNI_ProbeSets Man page
getNI_ProbeSets,INI_Calls-method Man page
getNI_ProbeSets-methods Man page
lFarms Man page Source code
onLoad Source code
plot Man page
plot,INI_Calls,missing-method Man page
plot-methods Man page
qFarms Man page Source code
summary Man page
summary,INI_Calls-method Man page
summary-methods Man page
testAffyBatch Man page Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/INIcalls-methods.R
R/farms.R
R/getI_Eset-methods.R
R/getI_ProbeSets-methods.R
R/getNI_Eset-methods.R
R/getNI_ProbeSets-methods.R
R/plot-methods.R
R/summary-methods.R
R/zzz.R
build
build/vignette.rds
data
data/testAffyBatch.rda
inst
inst/CITATION
inst/doc
inst/doc/farms.R
inst/doc/farms.Rnw
inst/doc/farms.pdf
man
man/INI_Calls-class.rd
man/INIcalls-methods.rd
man/dummy.Rd
man/expFarms.rd
man/generateExprVal.method.farms.rd
man/getI_Eset-methods.rd
man/getI_ProbeSets-methods.rd
man/getNI_Eset-methods.rd
man/getNI_ProbeSets-methods.rd
man/lFarms.rd
man/plot-methods.rd
man/qFarms.rd
man/summary-methods.rd
man/testAffyBatch.Rd
vignettes
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/farms.Rnw
vignettes/farms.bib
vignettes/farms_defs.sty
vignettes/natbib.bst
vignettes/natbib.sty
farms documentation built on May 20, 2017, 10:42 p.m.