affyPara: Parallelized preprocessing methods for Affymetrix Oligonucleotide Arrays
Version 1.36.0

The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.

AuthorMarkus Schmidberger <schmidb@ibe.med.uni-muenchen.de>, Esmeralda Vicedo <e.vicedo@gmx.net>, Ulrich Mansmann <mansmann@ibe.med.uni-muenchen.de>
Bioconductor views Microarray Preprocessing
Date of publicationNone
MaintainerMarkus Schmidberger <MSchmidberger@freenet.de>
LicenseGPL-3
Version1.36.0
URL http://www.ibe.med.uni-muenchen.de
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("affyPara")

Popular man pages

boxplotPara: Parallelized Box Plots for Microarray Data
computeExprSetPara: Parallel generate a set of expression values
MAplotPara: Parallelized relative M vs. A plots for Microarray Data
normalizeAffyBatchInvariantsetPara: Parallelized Invariante Set normalization
normalizeAffyBatchQuantilesPara: Parallelized quantile normalization
removeDistributedFiles: Remove distributed files from slaves
rmaPara: Parallelized PMA preprocessing
See all...

All man pages Function index File listing

Man pages

bgcPara: Parallelized Background Correction
boxplotPara: Parallelized Box Plots for Microarray Data
class.vsnInputPara: Class to contain input data and parameters for parallel vsn...
computeExprSetPara: Parallel generate a set of expression values
distributeFiles: Distribute files to slaves
MAplotPara: Parallelized relative M vs. A plots for Microarray Data
mergeSplitObjects: Merge a list of split objects
normalizeAffyBatchConstantPara: Parallelized scaling normalization
normalizeAffyBatchInvariantsetPara: Parallelized Invariante Set normalization
normalizeAffyBatchLoessPara: Parallelized loess normalization
normalizeAffyBatchLoessParaIter: Parallelized partial loess normalization with permutation
normalizeAffyBatchQuantilesPara: Parallelized quantile normalization
preproPara: Parallelized preprocessing
qa: Parallel Quality Assessment Summary
readAffybatchPara: Parallelized Read-AffyBatch function
removeDistributedFiles: Remove distributed files from slaves
rmaPara: Parallelized PMA preprocessing
snowReplace: Starting and Stopping SNOW Clusters
split: Functions to split objects into parts
vsnPara: Parallel fir of the vsn model

Functions

MAplotPara Man page Source code
MAplotParaSFgMean Source code
MAplotSer Man page Source code
ReadHeaderSF Source code
bgCorrectPara Man page Source code
bgCorrectParaSF Source code
boxplotPara Man page Source code
boxplotParaCalAllDiff Source code
boxplotParaCheckPercent Source code
boxplotParaCheckPercentSamples Source code
boxplotParaCheckTypDef Source code
boxplotParaChecknSamples Source code
boxplotParaComStatsM Source code
boxplotParaDrawn Source code
boxplotParaSFgParBox Source code
boxplotParacheckCritSamp Source code
boxplotParagCrSamp Source code
boxplotParagLimits Source code
boxplotParagMdMnDef Source code
boxplotParagMedIQR Source code
boxplotSplit Source code
calculateExprSetSF Source code
checkPartSize Source code
class:vsnInputPara Man page
combineMatrices Man page Source code
computeExprSetPara Man page Source code
createSumMatrix Source code
dim,vsnInputPara-method Man page
distributeFiles Man page Source code
doSummarizationPara Source code
drawHistDiff Source code
drawMAplot Source code
drawnBxp Source code
generateMatrizenSF Source code
getAffyBatchSF Source code
getArrayLoessSF Source code
getArraySF Source code
getBadQCLoessSigma Source code
getBoxplot Source code
getColSF Source code
getCompIntensityMatrixSF Source code
getCompIntensitySF Source code
getDifferenceBox Source code
getFUNAffyBatchSF Source code
getIntensitySF Source code
getLevelsBQ Source code
getMatrixBQBoxLevels Source code
getMatrixBQLevels Source code
getNumberPlots Source code
getObjectType Source code
getSumResults Source code
getTotalBoxToDrawn Source code
getValuesChips Source code
grad_loglikPara Source code
grad_loglikParaSF Source code
hirarchicalDistSF Source code
justvsnPara Man page Source code
logikPara Source code
logikParaSF1 Source code
logikParaSF2 Source code
makeCluster Man page Source code
mergeAffyBatches Man page Source code
ncol,vsnInputPara-method Man page
ndexValueL Source code
nitAffyBatchSF Source code
normalizeAffyBatchConstantPara Man page Source code
normalizeAffyBatchInvariantsetPara Man page Source code
normalizeAffyBatchLoessIterPara Man page Source code
normalizeAffyBatchLoessPara Man page Source code
normalizeAffyBatchQuantilesPara Man page Source code
normalizeConstantPara Source code
normalizeConstantParaSF1 Source code
normalizeConstantParaSF2 Source code
normalizeInvariantsetPara Source code
normalizeInvariantsetParaSF1 Source code
normalizeInvariantsetParaSF2 Source code
normalizeLoessIterPara Source code
normalizeLoessIterParaSFnodes Source code
normalizeLoessPara Source code
normalizeLoessParaSFbetNodes Source code
normalizeLoessParaSFnodes Source code
normalizeQuantilesPara Man page Source code
normalizeQuantilesParaSF1 Source code
normalizeQuantilesParaSF2 Source code
nrow,vsnInputPara-method Man page
onAttach Source code
onLoad Source code
permArrays Source code
permMatrix Source code
preproPara Man page Source code
read.affybatchPara Man page Source code
reassignMatrizenSF Source code
removeDistributedFiles Man page Source code
removeNA Source code
resetABSF Source code
resetMatSF Source code
rmaPara Man page Source code
rowMeansPara Source code
rowMeansParaSF Source code
rowVPara Source code
rowVParaSF Source code
setArraySF Source code
setColSF Source code
setIntMatSF Source code
setupPara Source code
setupParaSF Source code
splitAffyBatch Man page Source code
splitFileVector Man page Source code
splitMatrix Man page Source code
stopCluster Man page Source code
summaryM1M2Para Man page Source code
vsn2Para Man page Source code
vsn2_optimPara Source code
vsn2trsfPara Source code
vsn2trsfParaSF Source code
vsnColumnByColumnPara Source code
vsnColumnByColumnParaSF Source code
vsnInputPara Man page
vsnInputPara-class Man page
vsnLTSPara Source code
vsnMLPara Source code
vsnMatrixPara Source code
vsnSamplePara Source code
vsnStrataPara Source code
vsnrmaPara Man page Source code
writeArraySF Source code
writeLinesSF Source code
writeMeansArraySF Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/MAplotPara.R
R/MAplotParaFunctions.R
R/MAplotSer.R
R/affyParaIntern.R
R/bgcPara.R
R/boxplotPara.R
R/boxplotParaFunctions.R
R/combine.R
R/computeExprSetPara.R
R/distributeFiles.R
R/normalizeConstantPara.R
R/normalizeInvariantsetPara.R
R/normalizeLoessIterPara.R
R/normalizeLoessPara.R
R/normalizeQuantilesPara.R
R/preproPara.R
R/qa.R
R/readAffybatchPara.R
R/removeDistributedFiles.R
R/rmaPara.R
R/snowReplace.R
R/split.R
R/vsnPara.R
R/vsnParaFunctions.R
R/zzz.R
README
build
build/vignette.rds
inst
inst/doc
inst/doc/affyPara.R
inst/doc/affyPara.Rnw
inst/doc/affyPara.pdf
inst/doc/vsnStudy.R
inst/doc/vsnStudy.Rnw
inst/doc/vsnStudy.pdf
man
man/MAplotPara.Rd
man/bgcPara.Rd
man/boxplotPara.Rd
man/class.vsnInputPara.Rd
man/computeExprSetPara.Rd
man/distributeFiles.Rd
man/mergeSplitObjects.Rd
man/normalizeAffyBatchConstantPara.Rd
man/normalizeAffyBatchInvariantsetPara.Rd
man/normalizeAffyBatchLoessPara.Rd
man/normalizeAffyBatchLoessParaIter.Rd
man/normalizeAffyBatchQuantilesPara.Rd
man/preproPara.Rd
man/qa.Rd
man/readAffybatchPara.Rd
man/removeDistributedFiles.Rd
man/rmaPara.Rd
man/snowReplace.Rd
man/split.Rd
man/vsnPara.Rd
vignettes
vignettes/affyPara.Rnw
vignettes/fig
vignettes/fig/E-GEOD-11121
vignettes/fig/E-GEOD-11121/vsnAddonBoxplots_20-40-60.pdf
vignettes/fig/E-GEOD-11121/vsnAddon_20-40-60.pdf
vignettes/fig/E-GEOD-11121/vsnSubsamplesBoxplot_25.pdf
vignettes/fig/E-GEOD-11121/vsnSubsamples_25.pdf
vignettes/fig/E-GEOD-12093
vignettes/fig/E-GEOD-12093/vsnAddonBoxplots_20-40-60.pdf
vignettes/fig/E-GEOD-12093/vsnAddon_20-40-60.pdf
vignettes/fig/E-GEOD-12093/vsnSubsamplesBoxplot_50.pdf
vignettes/fig/E-GEOD-12093/vsnSubsamples_50.pdf
vignettes/fig/affyPara_speedup.pdf
vignettes/references.bib
vignettes/vsnStudy.Rnw
affyPara documentation built on May 20, 2017, 10:21 p.m.

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