[BioC] beadarray: mRNA QC help

Abhishek Pratap apratap at sagebase.org
Fri Jan 24 00:38:13 CET 2014

Hi All

I am trying to analyze some mRNA illumina bead level data through bead
array. Based on the detection p-values(plot attached): if I read it
right significant # probes
have no expression which concerns me but I could  have easily missed
some important step.

I am attaching the two box plots 1.) intensity and 2.)  probe level
detection p-values + code

Let me know your opinion.


beadlevel_data <- readIllumina(dir=dataDir, useImages=F,

#intensity boxplot
boxplot(beadlevel_data, transFun = logGreenChannelTransform, col = "green",
        ylab = expression(log[2](intensity)), las=2, outline=FALSE,
main= "Array intensities")

#summarize : detection p-val boxplot
BSData <- summarize(beadlevel_data)
det = calculateDetection(BSData)
boxplot(det, main='dset1_mRNA_probe_detection_pvals (Null: there is no
expression) ', ylab='p-value(detection score)',xaxt='n',
xlab='individual samples/array' )
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