[BioC] Help needed: Beadarray

Mark Dunning mark.dunning at gmail.com
Mon Apr 27 16:17:35 CEST 2009

Hi Jeanie,

The DiffScore function is no longer part of beadarray as we do all of
our analysis using the tools provided by the limma package .You should
be able to do the tests you want with limma, the user guide that comes
with the package is very helpful

I would definitely recommend working with bead-level data if you have
it. However, I don't find background normalization very helpful as it
increases variability at lower intensities and creates negative
intensities. If you do a log2 transformation (as one nearly always
does for microarray analysis) after background normalization then you
get a lot of missing values. The VST method in the lumi package is an
alternative to log2 and can cope with negative intensities, however
I've never really looked at whether doing VST with or without the
background normalization makes a difference.

Hope this helps,


On Wed, Apr 22, 2009 at 3:29 PM, Na, Jie <naj at ccf.org> wrote:
> 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?
> Thanks,
> Jeanie
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-apple-darwin8.11.1
> 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
> [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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