[BioC] discrepancy between BeadStudio images and beadarray imageplot

[Cei Abreu-Goodger]

Hi Luis,

I do hope you'll get a better response, but I can tell you that I found 
similar issues when analyzing mouse beadarrays. I think that the authors 
haven't tested the package as extensively for mouse as for human, and 
thus there a probably some problems in displaying the correct layout for 
these chips. So, it is my "guess" that the white streaks are artifacts 
generated by the package and do not reflect real artifacts on the array.

Cheers,

Cei

Luis Fernando Menezes 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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