[BioC] Detection calls with "beadarray"

Cei Abreu-Goodger cei at ebi.ac.uk
Tue Dec 2 15:13:53 CET 2008

Hello all,

I've just been trying to add detection calls to an 
"ExpressionSetIllumina" created with "beadarray". I couldn't find this 
mentioned in the vignettes, but found the function "calculateDetection" 
lying around.

Would this be the recommended way of using it? (near-working example, 
except that since the data contains no control-probes the actual 
detection values are left as NaN)

BSData <- setAnnotation(BSData,"Humanv1")
Detection(BSData) <- calculateDetection(BSData)
rownames(Detection(BSData)) <- featureNames(BSData)
colnames(Detection(BSData)) <- sampleNames(BSData)

Many thanks!


 > sessionInfo()
R version 2.8.0 (2008-10-20)


attached base packages:
[1] stats     graphics  grDevices datasets  tools     utils     methods
[8] base

other attached packages:
  [1] beadarray_1.10.0    sma_0.5.15          hwriter_0.93
  [4] geneplotter_1.20.0  annotate_1.20.1     xtable_1.5-4
  [7] AnnotationDbi_1.4.1 lattice_0.17-15     limma_2.16.3
[10] Biobase_2.2.1

loaded via a namespace (and not attached):
[1] DBI_0.2-4          KernSmooth_2.22-22 RColorBrewer_1.0-2 
[5] grid_2.8.0

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