exprReslt-class {puma} | 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 `ExpressionSet`.

### 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 `ExpressionSet`.
`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 `ExpressionSet` instance.
`notes`:
  Object of class "character" Vector of explanatory text

### 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

    ## 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")

[Package puma version 1.8.1 Index]