virtualArray: Build virtual array from different microarray platforms

This package permits the user to combine raw data of different microarray platforms into one virtual array. It consists of several functions that act subsequently in a semi-automatic way. Doing as much of the data combination and letting the user concentrate on analysing the resulting virtual array.

Author
Andreas Heider
Date of publication
None
Maintainer
Andreas Heider <aheider@trm.uni-leipzig.de>
License
GPL-3
Version
1.8.0

View on Bioconductor

Man pages

GPLs
Provides precompiled mappings of NCBI GEO platform IDs (GPLs)...
normalize.ExpressionSet.gq
gene quantiles normalization
normalize.ExpressionSet.mc
mean centering normalization
normalize.ExpressionSet.mrs
median rank scores normalization
normalize.ExpressionSet.nordi
normal discretization normalization
normalize.ExpressionSet.qd
quantile discretization normalization
sample_info_imported
sample_info data.frame object
virtualArrayBuildExprs
Format ExpressionSets as data.frames with identifiers in...
virtualArrayBuildfData
Collapses expression values according to given identifiers
virtualArrayBuildSampleInfo
Build data.frame suitable as "pData" for several...
virtualArrayComBat
Removes batch effects from microarray derived expression...
virtualArrayCompile
Compiles a single virtual array holding user provided...
virtualArrayDirs
Build virtualArray directory structure to hold raw data of...
virtualArrayExpressionSets
Combine different ExpressionSets into one
virtualArrayHclust
Plot a hclust object with colored labels
virtualArrayLoadRaw
Load user provided raw data files in the virtualArray...
virtualArrayMergeRecurse
Merge a list of data.frames by common rows
virtualArray-package
Combine raw data of several ExpressionSets into a "virtual...

Files in this package

virtualArray/DESCRIPTION
virtualArray/NAMESPACE
virtualArray/R
virtualArray/R/AllGenerics.R
virtualArray/R/Beta.NA.R
virtualArray/R/L.R
virtualArray/R/aprior.R
virtualArray/R/bprior.R
virtualArray/R/build.design.R
virtualArray/R/calculateOverlaps.R
virtualArray/R/design.mat.R
virtualArray/R/filter.absent.R
virtualArray/R/int.eprior.R
virtualArray/R/it.sol.R
virtualArray/R/list.batch.R
virtualArray/R/methods-virtualArrayComBat.R
virtualArray/R/more_batch_effect_removal_methods.R
virtualArray/R/onLoad.R
virtualArray/R/postmean.R
virtualArray/R/postvar.R
virtualArray/R/trim.dat.R
virtualArray/R/virtualArray-internal.R
virtualArray/R/virtualArrayBuildExprs.R
virtualArray/R/virtualArrayBuildSampleInfo.R
virtualArray/R/virtualArrayBuildSingleSampleInfo.R
virtualArray/R/virtualArrayBuildfData.R
virtualArray/R/virtualArrayCompile.R
virtualArray/R/virtualArrayDirs.R
virtualArray/R/virtualArrayExpressionSets.R
virtualArray/R/virtualArrayHclust.R
virtualArray/R/virtualArrayLoadRaw.R
virtualArray/R/virtualArrayMergeRecurse.R
virtualArray/build
virtualArray/build/vignette.rds
virtualArray/data
virtualArray/data/GPLs.RData
virtualArray/data/sysdata.rda
virtualArray/inst
virtualArray/inst/CITATION
virtualArray/inst/doc
virtualArray/inst/doc/virtualArray.R
virtualArray/inst/doc/virtualArray.Rnw
virtualArray/inst/doc/virtualArray.pdf
virtualArray/inst/extdata
virtualArray/inst/extdata/sample_info.txt
virtualArray/inst/extdata/sample_info_mod.txt
virtualArray/man
virtualArray/man/GPLs.Rd
virtualArray/man/normalize.ExpressionSet.gq.Rd
virtualArray/man/normalize.ExpressionSet.mc.Rd
virtualArray/man/normalize.ExpressionSet.mrs.Rd
virtualArray/man/normalize.ExpressionSet.nordi.Rd
virtualArray/man/normalize.ExpressionSet.qd.Rd
virtualArray/man/sample_info_imported.Rd
virtualArray/man/virtualArray-package.Rd
virtualArray/man/virtualArrayBuildExprs.Rd
virtualArray/man/virtualArrayBuildSampleInfo.Rd
virtualArray/man/virtualArrayBuildfData.Rd
virtualArray/man/virtualArrayComBat.Rd
virtualArray/man/virtualArrayCompile.Rd
virtualArray/man/virtualArrayDirs.Rd
virtualArray/man/virtualArrayExpressionSets.Rd
virtualArray/man/virtualArrayHclust.Rd
virtualArray/man/virtualArrayLoadRaw.Rd
virtualArray/man/virtualArrayMergeRecurse.Rd
virtualArray/vignettes
virtualArray/vignettes/virtualArray-016.pdf
virtualArray/vignettes/virtualArray.Rnw