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 ) )