Hi Krys:

    We have also seen a probe which has more than 3000 beads. This probe 
is not included in the bead manifest file 
(Mouse-6_v1_1_11234304_A_manifest.csv). However it might be worthwhile 
to check if this probe is one of the control probes in the file "control 
probe profile" output from BeadStudio.

Cheers,
Wei

Krys Kelly wrote:
> Hello
>
> 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.
>
> Krys
>
>
>
> Dr Krystyna A Kelly (Krys)
>  
> Department of Pathology
> University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
> Tel: 01223 333331
>
> and
>
> MRC Biostatistics Unit
> Institute of Public Health, Robinson Way, Cambridge CB2 0SR
> Tel: 01223 767408
>
> Email: kak28@cam.ac.uk
>
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