exprSetRG-class {arrayMagic}R Documentation

Class exprSetRG for two colour DNA microarray data (extension of exprSet)

Description

This is a class representation for two colour DNA microarray data. The class is based on the class exprSet of the Biobase package. The red and green channels are stored in a single exprSet object. The information on the corresponding red-green pairs is stored separately. Several class methods offer a convienent way to access and set data.

Creating Objects

new('exprSetRG',
channels = ..., # object of class matrix with columns "green" and "red"
exprs = ..., # object of class matrix
se.exprs = ..., # object of class matrix
phenoData= ..., # object of class phenoData
notes = ..., # object of class character
annotation = ..., # object of class character
)

Slots

indGreen:
Object of class vector; indexes of the green channel
indRed:
Object of class vector; indexes of the red channel
exprs:
Object of class matrix; the observed expression levels. This is a matrix with columns representing the red and green channels and rows representing genes. Each row in channels lists the indexes of the corresponding pair of red and green channels representing a single microarray slide.
se.exprs:
Object of class matrix; this is a matrix of the same dimensions as exprs, e.g. useful to represent the standard error estimates for the corresponding expression levels.
phenoData:
Object of class phenoData, i.e. an instance of class phenoData containing annotation information on the individual channels. The columns of the pData slot of this entity represent variables and the rows represent channels.
notes:
Object of class character containing explanatory text; default: ""
annotation:
Object of class character; default: ""

Extends

Class exprSet, directly.

Methods

show
(exprSetRG): renders information about the exprSetRG in a concise way on stdout, cf. class exprSet.
getExprSetLogRatio
(exprSetRG, seExprsHandling): Returns an exprSet object of the difference of the expression levels, i.e. the green channel minus the red channel. The phenoData slot it the result of calling the class method phenoDataSlide on the object exprSetRG. The se.exprs slot contains the root-mean-square or the mean of the se.exprs of both channels depending on the argument seExprsHandling. The root-mean-square might be useful if the two se.exprs values are estimated standard deviations based on the same number observations and identical distribution. seExprsHandling must be a character string; possible values are "rootMeanSquare" or "mean"; the default value is "rootMeanSquare".
getExprSetGreenMinusRed
same as method getExprSetLogRatio
getExprSetRedMinusGreen
similar to method getExprSetLogRatio; the "negative" difference of the expression levels is returned, i.e. the red channel minus the green channel.
getExprSetGreen
(exprSetRG): Returns an exprSet object which contains the expression levels of the green channel and the corresponding annotation.
getExprSetRed
(exprSetRG): Returns an exprSet object which contains the expression levels of the red channel and the corresponding annotation.
phenoDataSlide
(exprSetRG): Returns an phenoData object characterizing all microarray slides. Those annotation information, which is the same for both channels (and not NA) is taken directly, e.g. the the slide number. All other annotation variables are added specifically for each channel, i.e. prefixed with "greenSpecific_" and "redSpecific_". Do not use varLabels-names for subsetting.
pDataSlide
(exprSetRG): Returns an pData object, i.e. pData(phenoDataSlide(exprSetRG)); cf. phenoDataSlide. Do not use varLabels-names for subsetting.
phenoDataGreen
(exprSetRG): Returns an phenoData object of the annotation information given for the green channel. Do not use varLabels-names for subsetting.
pDataGreen
(exprSetRG): Returns the pData object taken out of the result of calling phenoDataGreen. Do not use varLabels-names for subsetting.
phenoDataRed
(exprSetRG): Returns an phenoData object of the annotation information given for the red channel. Do not use varLabels-names for subsetting.
pDataRed
(exprSetRG): Returns the pData object taken out of the result of calling phenoDataRed. Do not use varLabels-names for subsetting.
slideSubset
(exprSetRG,i,j): Subsetting operation; where i corresponds to the rows and j corresponds to the microarray slides. j is given by indexes or logicals related to the order of the channel pairs in channels; cf. the constructor slot channels.
getIndGreen
(exprSetRG): An accessor function for slot indGreen. The corresponding elements of indGreen and indRed define microarray slides.
getIndRed
(exprSetRG): An accessor function for slot indRed. The corresponding elements of indGreen and indRed define microarray slides.
[
(exprSetRG,i,j,type): A subset operator. Ensures that both the data and the annotation information (phenoData) are subseted properly. This may only mix up the pairing of the channels, i.e. the validity of an exprSetRG, if you use argument option type == "invalidExprSetRG". Default: "validExprSetRG". See also: slideSubset.
cbind
(...): Concatenates exprSetRG objects. Genes (rows) are assumed to match; cf. cbind.exprSetRG
as.exprSet
(exprSetRG): Class cast, returns an object of exprSet, the information on the red and green channels is discarded.
as.RGList
(exprSetRG, func): Returns an object of RGList which in general refers to raw data. Hence, func(expression values) is returned, i.e. exp(x) by default. All background values in the RGList object are set to zero.

Author(s)

Andreas Buness <a.buness@dkfz.de>

See Also

exprSet-class, arrayData-class

Examples

  indGreen=1:3
  indRed=4:6
  channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
  colnames(channels) <- c("green","red")
  eSA <- new("exprSetRG", exprs=matrix(1:60, ncol=6, nrow=10), phenoData=
          new("phenoData", pData=data.frame(matrix(0,nrow=6,ncol=1)),
              varLabels=list(rep("varLabel1",1))), channels=channels)
  stopifnot( all(pDataSlide(eSA) ==pData(eSA)[1:3,,drop=FALSE]) )
  eSAGreen <- getExprSetGreen(eSA)
  eSARed <- getExprSetRed(eSA)
  eSALogRatio <- getExprSetLogRatio(eSA)
  eSALogRatio2 <- getExprSetGreenMinusRed(eSA)
  eSALogRatio3 <- getExprSetRedMinusGreen(eSA)
  stopifnot( identical( eSALogRatio, eSALogRatio2 ) )
  stopifnot( identical( exprs(eSALogRatio), exprs(eSAGreen)-exprs(eSARed)) )
  stopifnot( all.equal.numeric( as.vector(exprs(eSALogRatio3)), as.vector(exprs(eSARed)-exprs(eSAGreen)) ))
  eSAPart <- eSA[,c(1,3,1,4,6,4)]
  eSAInvalid <- eSA[,c(1,3,1,5,6,4),type="invalidExprSetRG"]
  eSAPart2 <- slideSubset(eSA,j=c(1,3,1))

  eSAeSA <- cbind(eSA, eSA)
  eSAeSAPart2 <- cbind(eSA, eSAPart2)
  stopifnot( class(as.exprSet(eSA)) == "exprSet" )

  
 

[Package arrayMagic version 1.16.1 Index]