[BioC] discrepancy between BeadStudio images and beadarray imageplot

Luis Fernando Menezes lmenezes at jhmi.edu
Thu Mar 5 03:13:21 CET 2009


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,


 > sessionInfo()
R version 2.8.0 Patched (2008-10-22 r46776)


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         
  [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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