[BioC] Question about beadarray package for mouse ref V2 illumina beadarray

[Yiwen Chen]

Hi,

I was trying to use beadarray package to process bead-level data from
mouse refV2 illumina single-color beadarray. According to the manual, I
first read in the background-subtracted data directly from csv data and
then generate beadsummary data. However, the boxplot of log2 of
beadsummary data looks almost the same as the un-logged
background-subtracted bead-level data.
I was very confused about it and hope someone could point out the possible
reasons. I have attached the boxplot of un-logged background-substracted
bead-level data, log2 bead-summary data and un-logged bead-summary data.
I also pasted the script and sessionInfo.

Thank you very much.

Best,
Yiwen

"""
library(beadarray)
targets=read.table("targets.txt",sep="\t",header=TRUE,as.is=TRUE)
BLData=readIllumina(arrayNames=targets$ArrayName,textType=".csv",targets=targets,useImages=FALSE,backgroundMethod="none",annoPkg="Mousev2")
BSData=createBeadSummaryData(BLData,imagesPerArray=1)
par(mfrow=c(1,3),mai=c(2,0.5,0.2,0.1))
boxplotBeads(BLData,las=2,outline=FALSE,ylim=c(4,8),main="Background
Corrected")
boxplot(as.data.frame(log2(exprs(BSData))),outline=FALSE,ylim=c(4,8),ylab="log2(intensity)",main="Bead
summary data")
boxplot(as.data.frame(exprs(BSData)),outline=FALSE,ylim=c(16,64),ylab="log2(intensity)",main="Bead
summary data")


> sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] beadarray_1.12.1 hwriter_1.1      Biobase_2.4.1

loaded via a namespace (and not attached):
[1] limma_2.18.0 tools_2.9.0
"""

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