slideMerge {arrayMagic} | R Documentation |
exprSetArrayObject |
object of class exprSetArray |
slideMergeVariable |
character string specifying the variable of the phenoData used to determine replicas |
sampleAnnotationColumns |
vector of character strings; containing all phenoData variables relevant for further analysis. The annotation should be consistent for replicas. By default all phenoData variables are taken, i.e. sampleAnnotationColumns is missing. |
modified exprSetArrayObject
Andreas Buness <a.buness@dkfz.de>
indCy3=1:4 indCy5=5:8 channels <- matrix( c(indCy3,indCy5), nrow=length(indCy3), byrow=FALSE ) colnames(channels) <- c("Cy3","Cy5") myMatrix <- matrix(c(1:8,rep(1:4,2),c(1,1,1,4,2,2,2,2),c(2,2,2,2,4,1,1,1) ,rep(c(1,1,2,2),2)),nrow=8,ncol=5,byrow=FALSE) colnames(myMatrix) <- c("one","two","three","four","merge") exprsMatrix <- matrix(rep(1:10,4), ncol=8, nrow=5, byrow=FALSE) eSA <- new("exprSetArray", exprs=exprsMatrix, phenoData= new("phenoData", pData=data.frame(myMatrix), varLabels=as.list(colnames(myMatrix))), channels=channels) eSM <- slideMerge(exprSetArrayObject=eSA, slideMergeVariable="merge") stopifnot( all( dim(exprs(eSM)) == c(5,4) ) ) stopifnot( all(as.matrix(pData((phenoDataSlide(eSM)[,which(varLabels(phenoDataSlide(eSM)) == "slidesInGroup")]))) == matrix(c("1;2","3;4"),ncol=1,nrow=2)) ) exprs(eSM) stopifnot( all(exprs(getExprSetCy3(eSM)) == cbind(rowMeans(exprs(getExprSetCy3(eSA))[,1:2]), rowMeans(exprs(getExprSetCy3(eSA))[,3:4])))) stopifnot( all(exprs(getExprSetCy5(eSM)) == cbind(rowMeans(exprs(getExprSetCy5(eSA))[,1:2]), rowMeans(exprs(getExprSetCy5(eSA))[,3:4])))) stopifnot(se.exprs(getExprSetCy3(eSM)) == cbind(as.matrix(apply((exprs(getExprSetCy3(eSA))[,1:2]),1,sd)), as.matrix(apply((exprs(getExprSetCy3(eSA))[,3:4]),1,sd)))) stopifnot(se.exprs(getExprSetCy5(eSM)) == cbind(as.matrix(apply((exprs(getExprSetCy5(eSA))[,1:2]),1,sd)), as.matrix(apply((exprs(getExprSetCy5(eSA))[,3:4]),1,sd)))) # one and two are inconsistent in both channels stopifnot( all(unlist(varLabels(phenoDataSlide(eSM))) == c("one","two","merge","slidesInGroup")) )