Entering edit mode
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,illuminaOut
lierMethod,myMean,mySe,"G")
for (iChip in 1:nChips)
{
setwd(Chip.Dir[iChip])
BLData = readIllumina(useImages=FALSE,
illuminaAnnotation="Humanv4")
BSData <- summarize(BLData,list(greenChannel),useSampleFac=TRU
E,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
