| slideMerge {arrayMagic} | R Documentation |
The mean of the expression values is calculated
separately for each channel.
If no se.exprs values are given
in exprSetRGObject,
se.exprs is set to the standard deviation
of the expression values
(which is possibly NA).
If available it is set to the root-mean-square
or the mean of the given se.exprs
values depending on the
argument seExprsHandling.
The root-mean-square can be useful if the
se.exprs values are estimated standard deviations
based on the same number observations taken from identical
distributions.
slideMerge(exprSetRGObject, slideMergeColumn, sampleAnnotationColumns, seExprsHandling="rootMeanSquare", verbose=TRUE)
exprSetRGObject |
object of class exprSetRG;
required; default missing |
slideMergeColumn |
character string specifying the variable
of the phenoData object of the exprSetRGObject,
which is used to determine replicas; required; default missing |
sampleAnnotationColumns |
vector of character strings;
optional; default missing.
A vector which contains all phenoData variables
relevant for further analysis.
The phenoData-annotation should be consistent for replicas.
By default the argument sampleAnnotationColumns is missing
and all phenoData variables are used. |
seExprsHandling |
character string; either "rootMeanSquare" or "mean"; required; default "rootMeanSquare" |
verbose |
logical; required; default: TRUE |
object of class exprSetRG-class, i.e.
the "merged" exprSetRGObject
Andreas Buness <a.buness@dkfz.de>
indGreen=1:2
indRed=3:4
channels <- matrix( c(indGreen,indRed), nrow=length(indGreen), byrow=FALSE )
colnames(channels) <- c("green","red")
exprsMatrix <- matrix(rep(1:10,4),nrow=10,ncol=4,byrow=FALSE)
phenoMatrix <- matrix(c(c(1,2),c(3,3),c(5,5)),nrow=2,ncol=3,byrow=FALSE)
colnames(phenoMatrix) <- c("one","two","usedForMerge")
phenoMatrix <- rbind(phenoMatrix,phenoMatrix)
eSA <- new("exprSetRG", exprs=exprsMatrix, phenoData=
new("phenoData", pData=data.frame(phenoMatrix),
varLabels=as.list(colnames(phenoMatrix))),
channels=channels)
eSM <- slideMerge(exprSetRGObject=eSA, slideMergeColumn="usedForMerge")
eSAOne <- slideSubset(eSA,j=c(1))
stopifnot( all(exprs(eSAOne) == exprs(eSM) ))
stopifnot( all( se.exprs(eSM) == 0 ) )