exprReslt-class: Class exprReslt

In puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Description

This is a class representation for Affymetrix GeneChip probe level data. The main component are the intensities, estimated expression levels and the confidence of expression levels from multiple arrays of the same CDF type. In extends ExpressionSet.

Objects from the Class

Objects can be created by calls of the form new("exprReslt", ...).

Fields

prcfive:

Object of class "matrix" representing the 5 percentile of the observed expression levels. This is a matrix with columns representing patients or cases and rows representing genes.

prctwfive:

Object of class "matrix" representing the 25 percentile of the observed expression levels. This is a matrix with columns representing patients or cases and rows representing genes.

prcfifty:

Object of class "matrix" representing the 50 percentile of the observed expression levels. This is a matrix with columns representing patients or cases and rows representing genes.

prcsevfive:

Object of class "matrix" representing the 75 percentile of the observed expression levels. This is a matrix with columns representing patients or cases and rows representing genes.

prcninfive:

Object of class "matrix" representing the 95 percentile of the observed expression levels. This is a matrix with columns representing patients or cases and rows representing genes.

phenoData:

Object of class "phenoData" inherited from ExpressionSet.

annotation:

A character string identifying the annotation that may be used for the ExpressionSet instance.

Extends

Class "ExpressionSet", directly.

Methods

se.exprs

signature(object = "exprReslt"): obtains the standard error of the estimated expression levels.

se.exprs<-

signature(object = "exprReslt"): replaces the standard error of the estimated expression levels.

prcfifty

signature(object = "exprReslt"): obtains the 50 percentile of the estimated expression levels.

prcfifty<-

signature(object = "exprReslt"): replaces the 50 percentile of the estimated expression levels.

prcfive

signature(object = "exprReslt"): obtains the 5 percentile of the estimated expression levels.

prcfive<-

signature(object = "exprReslt"): replaces the 5 percentile of the estimated expression levels.

prcninfive

signature(object = "exprReslt"): obtains the 95 percentile of the estimated expression levels.

prcninfive<-

signature(object = "exprReslt"): replaces the 95 percentile of the estimated expression levels.

prcsevfive

signature(object = "exprReslt"): obtains the 75 percentile of the estimated expression levels.

prcsevfive<-

signature(object = "exprReslt"): replaces the 75 percentile of the estimated expression levels.

prctwfive

signature(object = "exprReslt"): obtains the 25 percentile of the estimated expression levels.

prctwfive<-

signature(object = "exprReslt"): replaces the 25 percentile of the estimated expression levels.

show

signature(object = "exprReslt"): renders information about the exprReslt in a concise way on stdout.

write.reslts

signature(x = "exprReslt"): writes the expression levels and related confidences to files. It takes the same arguments as write.table. The argument "file" does not need to set any extension. The different file marks and extension "csv" will be added automatically. The default file name is "tmp". In the final results, expression levels are in the file "tmp\_exprs.csv", standard deviations in "tmp\_se.csv", 5 percentiles in "tmp\_prctile5.csv", likewise, 25, 50, 75 and 95 percentiles in "tmp\_prctile25.csv", "tmp\_prctile50.csv", "tmp\_prctile75.csv" and "tmp\_prctile95.csv" respectively.

Author(s)

Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence, Richard D. Pearson

See Also

Related method mmgmos and related class ExpressionSet.

Examples

if(FALSE){
## load example data from package affydata
#	Next 4 lines commented out to save time in package checks, and saved version used
# if (require(affydata)) {
#	data(Dilution)
#	eset_mmgmos <- mmgmos(Dilution)
# }
data(eset_mmgmos)

## save the expression results into files
write.reslts(eset_mmgmos, file="example")
}

puma documentation built on Nov. 8, 2020, 11:08 p.m.