exprReslt-class {mmgmos}R Documentation

Class exprReslt

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 exprSet-class.

Objects from the Class

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

Slots

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.
exprs:
Object of class "matrix" representing the observed expression levels. This is a matrix with columns representing patients or cases and rows representing genes.
se.exprs:
Object of class "matrix" representing the standard deviation 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 exprSet.
description:
Object of class "MIAME". For compatibility with previous version of this class description can also be a "character". The class characterOrMIAME has been defined just for this.
annotation:
A character string identifying the annotation that may be used for the exprSet instance.
notes:
Object of class "character" Vector of explanatory text

Extends

Class "exprSet", directly.

Methods

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.

Note

This class is better described in the vignette.

Author(s)

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

See Also

Related method mmgmos and related class exprSet-class.

Examples

## load example data from package Affy
data(affybatch.example)

## use method mmgmos to calculate the expressiong levels and related confidences 
## of the measures for affybatch.example
eset<-mmgmos(affybatch.example)

## save the expression resluts into files
write.reslts(eset, file="example")

[Package mmgmos version 1.2.0 Index]