[BioC] Using beadarray for bead level data, what is the ProbeID with 1000's of beads?

Krys Kelly kak28 at cam.ac.uk
Fri Nov 2 13:34:56 CET 2007


I have data from 5 Illumina mouse 6 beadarray slides.  I have read in the
bead level data using the beadarray package and used tapply to count the
number of beads per probe.

As an example, the output below is the summary and the top 10 counts for the
first strip of the first array of my first slide.

> summary(beadsPerProbe1[1,])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   7.00   30.00   35.00   35.71   41.00 3470.00 

> s <- sort(beadsPerProbe1[1,], decreasing=TRUE)

> s[1:10]
 [1] 3470   90   81   79   78   78   78   78   78   75

Unexpectedly (to me at least), there is one ProbeID with 3470 beads.  

There is a single ProbeID with a bead count > 3000 for each of the 60
strips.  The probeID is different in every case.  The data (e.g.
BLData39A[[1]]$G) for the ProbeIDs with these high bead counts looks like
sensible data.  

Does anyone know the meaning of this ProbeID with these high counts?

I haven't included my code and sessionInfo() because I think this is a
feature of the array rather than a programming error.

Thanks for any help.


Dr Krystyna A Kelly (Krys)
Department of Pathology
University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
Tel: 01223 333331


MRC Biostatistics Unit
Institute of Public Health, Robinson Way, Cambridge CB2 0SR
Tel: 01223 767408

Email: kak28 at cam.ac.uk

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