virtualArrayCompile: Compiles a single virtual array holding user provided...

In virtualArray: Build virtual array from different microarray platforms

Description

The function takes ExpressionSets of rawdata provided by the "virtualArrayLoadRaw" function together with annotation data.frames provided by the function "virtualArray.load.annot" and matches the rawdata on the basis of the given identifier. Currently only "Gene.Symbol" is supported by "virtualArrayCompile" but this will be extendend in future versions. Meanwhile you can use "virtualArray.ExpressionSet" to use other identifiers.

Usage

virtualArrayCompile(root_dir = getwd(), identifier = "Gene.Symbol", covars= 3, virtualArray = virtualArray)

Arguments

root_dir	The top level directory holding the rawdata and the "sample_info.txt" file.
identifier	The annotation identifier based on which the comparison between the different platforms is made.
covars	Numer of columns to read from "sample_info" data.frame or ".txt". Defaults to 3, which denotes only to use the sample/array naming and the "Batch" column. A 4 expects the "Covariate.1" column to be filled with meaningful information regarding grouping of samples. When the value is the character vector "all" even more columns can be used.
virtualArray	A list which holds the intermediate output of the "virtArray" package. It contains both raw data as well as annotation data.frames. It defaults to "virtualArray" but can be any other name.

Value

An ExpressionSet is created, holding data of all supplied microarray platforms.

Author(s)

Andreas Heider (2011)

See Also

virtualArray-package, virtualArray.ExpressionSet, virtualArrayCompile

Examples

# This is example is commented out, because it would slow down building the package!
# virtualArrayDirs()
# getGEOSuppFiles(baseDir="rawdata/Affymetrix/U133Plus2/",makeDirectory=F,GEO="GSM589512")
# gunzip(filename="rawdata/Affymetrix/U133Plus2/GSM589512.CEL.gz",remove=T)
# getGEOSuppFiles(baseDir="rawdata/Affymetrix/U133A/",makeDirectory=F,GEO="GSM589506")
# getGEOSuppFiles(baseDir="rawdata/Affymetrix/U133A/",makeDirectory=F,GEO="GSM589509")
# gunzip(filename="rawdata/Affymetrix/U133A/GSM589506.CEL.gz",remove=T)
# virtualArray <- virtualArrayLoadRaw()
# my_ExpressionSet <- virtualArrayCompile(virtualArray=virtualArray)

virtualArray documentation built on Sept. 12, 2016, 6:10 a.m.