[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)
library(beadarray)
data(BSData)
BSData <- setAnnotation(BSData,"Humanv1")
Detection(BSData) <- calculateDetection(BSData)
rownames(Detection(BSData)) <- featureNames(BSData)
colnames(Detection(BSData)) <- sampleNames(BSData)
Many thanks!
Cei
> sessionInfo()
R version 2.8.0 (2008-10-20)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
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
RSQLite_0.7-1
[5] grid_2.8.0
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