[BioC] summarized expression values from beadarray versus GenomeStudio

[Ina Hoeschele]

Hi Mark et al.,
  I have calculated correlations among the expression vectors of different samples (in particular for a control sample that we use on each BeadChip), both for the expression data that I have processed in Bioconductor using the beadarray package and for the expression data produced by GenomeStudio (selecting quantile normalization). The correlations (especially for the control samples from different chips) are clearly worse for the Bioconductor processed data and I have been trying to track down where I have a problem.

I also have the summarized (bead-type) intensities from GenomeStudio without normalization. I obtain the corresponding summarized values from beadarray with the following code 

myMean = function(x) mean(x, na.rm = TRUE)
mySe = function(x) sd(x, na.rm = TRUE)/sqrt(length(x))
GreenChannelTransform <- function (BLData, array)
{
	x = getBeadData(BLData, array = array, what = "Grn")
	return(x)
}
greenChannel = new("illuminaChannel",GreenChannelTransform,illuminaOutlierMethod,myMean,mySe,"G")

for (iChip in 1:nChips)
{
	setwd(Chip.Dir[iChip])
	BLData = readIllumina(useImages=FALSE, illuminaAnnotation="Humanv4")
	BSData <- summarize(BLData,list(greenChannel),useSampleFac=TRUE,sampleFac=NULL,removeUnMappedProbes=TRUE)
	save(BSData,file="BSData.rda")
	rm(BLData); rm(BSData); gc()
}


If the data are summarized in this way using Bioconductor/beadarray, would you not expect the summarized values to be identical to those from GenomeStudio?

I checked the summarized value for one beadtype on the first several sections of chip 1. 
The summary values from GenomeStudio are: 77.93, 159.16, 174.93, 131.05, 484.39
The summary values from beadarray are: 90.0, 192.0, 1q88.5, 157.0, 492.0
(I also calculated the first summary value by hand and come up with 103.36!)

Why are these values different, any hint?

Many thanks as always, Ina