attachExpr-methods: Attach/Remove Expression Measures

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

Attach/remove expression levels to/from ExprTreeSet.

Usage

attachExpr(object, treenames = "*")

removeExpr(object)

Arguments

object	Object of class "ExprTreeSet".
treenames	Object of class "list" representing the names of the ROOT expression trees.

Details

By default expression levels will be saved in class ExprTreeSet as slot data, since usually the data.frame obtained as result of e.g. rma normalization is of reasonable size. However, when normalizing many arrays, especially exon arrays at probeset levels, it may be better to compute rma with slot add.data=FALSE thus avoiding memory problems. In this case, function attachExpr allows to fill slot data on demand.

attachExpr exports expression levels from expression trees from ROOT expression file and and saves as data.frame data. treenames is a vector of tree names to attach; for treenames="*" all trees from slot treenames will be exported and expression levels attached as data.frame data.

removeExpr removes expression levels from ExprTreeSet and replaces data.frame data with an empty data.frame of dim(0,0).

Value

A ExprTreeSet object.

Note

Do not use attachExpr unless you know that your computer has sufficient RAM, especially when using exon arrays. It may be advisible to use a subset of treenames only.

Author(s)

Christian Stratowa

See Also

attachCall, removeCall

Examples

## first, load ROOT scheme file and ROOT data file
scheme.test3 <- root.scheme(paste(path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
data.test3 <- root.data(scheme.test3, paste(path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

data.rma <- rma(data.test3,"tmp_Test3RMA0",tmpdir="",background="pmonly",normalize=TRUE,add.data=FALSE,verbose=FALSE)

## attach data
data.rma <- attachExpr(data.rma)

## get data.frame
expr.rma <- validData(data.rma)
head(expr.rma)

## remove data
data.rma <- removeExpr(data.rma)

rm(scheme.test3, data.test3)
gc()

xps documentation built on Nov. 8, 2020, 6 p.m.