[BioC] Help needed: Beadarray

Na, Jie naj at ccf.org
Wed Apr 22 16:29:42 CEST 2009

Hi list,

I have questions about beadarray package that I hope to get some answer or
helpful hint from this list.

1. Where is the function DiffScore? I don't seem to be able to find this
function although it was mentioned in the document "beadarray: An R package
to Analyse Illumina BeadArrays"2006.
2. I want to make pair-wise comparisons between arrays.  I have the bead
level data available.
A. Is background subtraction with background normalization is recommended?
B. If here is no such function of DiffScore existing any more, should I do
modified t-test on the summarized data on the beadlevel data?



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


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

other attached packages:
 [1] lumi_1.8.3           RSQLite_0.7-1        DBI_0.2-4
 [4] preprocessCore_1.4.0 mgcv_1.4-1           affy_1.20.0
 [7] beadarray_1.10.0     sma_0.5.15           hwriter_0.93
[10] geneplotter_1.20.0   annotate_1.20.1      xtable_1.5-4
[13] AnnotationDbi_1.4.2  lattice_0.17-17      Biobase_2.2.1
[16] limma_2.16.3  

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-22 RColorBrewer_1.0-2 affyio_1.10.1
[4] grid_2.8.0 


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