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 of 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 slide 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 |
The phenoData
-annotation should be consistent for slide replicas,
The annotation within the group of replicas is checked for consistency
to assure a meaningful slide merge operation. Any ambiguities are
reported. This reporting shall help to avoid and discover slide
annotation errors. For example if samples are hybridized twice,
the "slideNumber" will not be consistent within the "sampleID"
which is used to determine replicas via the argument
slideMergeColumn
.
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, check.names=FALSE), 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 ) )