[BioC] discrepancy between BeadStudio images and beadarray imageplot

Luis Fernando Menezes lmenezes at jhmi.edu
Thu Mar 5 21:00:30 CET 2009

Thank you for you comments, Mark and Cei.
Just another quick question: the number of beads per probe that are  
detected in the different arrays of the 8-array slide is slightly  
lower in the the array with the white streaks compared with a "normal"  
array in the same slide (median:36 vs. 41; min: 9 vs. 13). Could this  
potentially bias the analysis (I'm using lumi) in such a way that I  
should ask Illumina to replace the array? And, if so, is this a common  
enough problem with Illumina to raise concerns about the reliability/ 
reproducibility of this platform?
Thanks again,


On Mar 5, 2009, at 5:28 AM, Mark Dunning wrote:

> Hi Luis,
> The white streaks you see on the imageplots are because of missing
> data on the array. This occurs when the Illumina scanner is unable to
> decode the identity of beads on the array. Information about these
> undecoded beads is not reported in the output that comes out from the
> scanner and therefore we cannot use them in any analysis, including
> The white streaks would not show up in the BeadStudio images or the
> TIFF images generated by the scanner as these are just the raw pixel
> intensities and do not take bead identity into account.
> Hope this helps
> Regards,
> Mark
> On Thu, Mar 5, 2009 at 2:13 AM, Luis Fernando Menezes <lmenezes at jhmi.edu 
> > wrote:
>> Hello.
>> I have been using beadarray (v. 1.10.0)  to analyze some Illumina  
>> mouse
>> ref8v2 arrays.
>> When I import the images and expression data using readIllumina()  
>> and plot
>> them using imageplot() [either before or after background  
>> subtraction], I
>> get an unusual pattern that would suggest some sort of artifact in  
>> the
>> array, with "white streaks" across it.
>> When I questioned the core who had done the microarray experiment,  
>> they said
>> the BeadStudio image did not show any of the odd patterns.
>> Using outlierPlot() or BASH, some areas were flagged for masking,  
>> but they
>> did not match the "white streak areas" (I assume that is because the
>> outliers would in general have increased expression levels, as  
>> opposed to
>> the white areas with almost no signal).
>> My questions are:
>> 1) is there any reason why the images generated by BeadStudio and  
>> beadarray
>> should be different?
>> 2) why are the streaks with almost no signal not flagged as regions  
>> that
>> should be masked?
>> 3) should I be concerned about these low signal streaks?
>> Thank you. Best regards,
>> Luis.
>>> sessionInfo()
>> R version 2.8.0 Patched (2008-10-22 r46776)
>> i386-apple-darwin9.5.0
>> locale:
>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets   
>> methods
>> base
>> other attached packages:
>>  [1] beadarray_1.10.0    sma_0.5.15          hwriter_0.93
>>  geneplotter_1.20.0  annotate_1.20.0     xtable_1.5-4
>>  AnnotationDbi_1.4.1
>>  [8] lattice_0.17-15     Biobase_2.2.0       limma_2.16.2
>> loaded via a namespace (and not attached):
>> [1] DBI_0.2-4          KernSmooth_2.22-22 RColorBrewer_1.0-2  
>> RSQLite_0.7-0
>>    grid_2.8.0
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