[BioC] discrepancy between BeadStudio images and beadarray imageplot

[Mark Dunning]

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
BASH.

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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