mas4: MAS 4.0 Expression Measure

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

Description

This function converts a DataTreeSet into an ExprTreeSet using the XPS implementation of Affymetrix's MAS 4.0 expression measure.

Usage

mas4(xps.data,
     filename   = character(0),
     filedir    = getwd(),
     tmpdir     = "",
     normalize  = FALSE,
     sc         = 500,
     option     = "transcript",
     exonlevel  = "",
     update     = FALSE,
     xps.scheme = NULL,
     add.data   = TRUE,
     verbose    = TRUE)

xpsMAS4(object, ...)

Arguments

xps.data	object of class DataTreeSet.
filename	file name of ROOT data file.
filedir	system directory where ROOT data file should be stored.
tmpdir	optional temporary directory where temporary ROOT files should be stored.
normalize	logical. If TRUE scale normalization is used after an ExprTreeSet is obtained.
sc	value at which all arrays will be scaled to.
option	option determining the grouping of probes for summarization, one of ‘transcript’, ‘exon’, ‘probeset’; exon arrays only.
exonlevel	exon annotation level determining which probes should be used for summarization; exon/genome arrays only.
update	logical. If TRUE the existing ROOT data file filename will be updated.
xps.scheme	optional alternative SchemeTreeSet.
add.data	logical. If TRUE expression data will be included as slot data.
verbose	logical, if TRUE print status information.
object	object of class DataTreeSet.
...	arguments filename,filedir,tmpdir,option,exonlevel,xps.scheme.

Details

This function computes the Affymetrix MAS 4.0 expression measure, i.e. the ‘Average Difference’ expression level, as implemented in XPS.

If normalize=TRUE then the expression levels will be scaled to sc. For sc=0 the expression levels will be scaled to the mean expression level.

xpsMAS4 is the DataTreeSet method called by function mas4, however, expression levels will not be scaled to a common mean expression level.

For further details see mas5.

Value

An ExprTreeSet

Note

In contrast to function mas4, expression levels computed with xpsMAS4 will not be scaled to a common mean expression level.

Author(s)

Christian Stratowa

References

Affymetrix (1999) GeneChip Expression Analysis Algorithm Tutorial, Affymetrix Inc., Santa Clara, CA.

See Also

xpsMAS4, express

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.mas4 <- mas4(data.test3,"tmp_Test3MAS4",tmpdir="",normalize=TRUE,sc=500, update=TRUE,verbose=FALSE)

## get data.frame
expr.mas4 <- validData(data.mas4)
head(expr.mas4)

## plot results (negative expression values!)
if (interactive()) {
boxplot(expr.mas4)
}

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

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