exprSetRG-class {arrayMagic} | R Documentation |
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.
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
)
indGreen
:vector
; indexes of the
green channelindRed
:vector
; indexes of the
red channelexprs
: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
: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
: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
:character
containing
explanatory text; default: ""annotation
:character
;
default: ""
Class exprSet
, directly.
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". getExprSetLogRatio
getExprSetLogRatio
; the "negative" difference
of the expression levels is returned, i.e. the red
channel minus the green channel.
exprSet
object which contains the expression levels of the green channel
and the corresponding annotation.exprSet
object which contains the expression levels of the red channel
and the corresponding annotation.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.pData
object, i.e. pData(phenoDataSlide(exprSetRG))
;
cf. phenoDataSlide
.
Do not use varLabels-names for subsetting.phenoData
object of the annotation information given for the green channel.
Do not use varLabels-names for subsetting.pData
object taken out of the result of calling phenoDataGreen
.
Do not use varLabels-names for subsetting.phenoData
object of the annotation information given for the red channel.
Do not use varLabels-names for subsetting.pData
object taken out of the result of calling phenoDataRed
.
Do not use varLabels-names for subsetting.channels
;
cf. the constructor slot channels
.indGreen
. The corresponding elements of indGreen and indRed
define microarray slides.indRed
. The corresponding elements of indGreen and indRed
define microarray slides.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
.exprSetRG
objects.
Genes (rows) are assumed to match;
cf. cbind.exprSetRG
exprSet
, the information on the red and green channels
is discarded.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.
Andreas Buness <a.buness@dkfz.de>
exprSet-class
,
arrayData-class
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" )