slideMerge {arrayMagic} | R Documentation

## Averaging of two colour microarray replicas

### Description

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.

### Usage

    slideMerge(exprSetRGObject, slideMergeColumn, sampleAnnotationColumns, seExprsHandling="rootMeanSquare", verbose=TRUE)

### Arguments

`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`

### Details

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`.

### Value

object of class `exprSetRG-class`, i.e. the "merged" `exprSetRGObject`

### Author(s)

Andreas Buness <a.buness@dkfz.de>

### See Also

`spotMerge`, `exprSetRG-class`

### Examples

      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 ) )

[Package arrayMagic version 1.5.4 Index]