[BioC] beadarray: outliers but not summary in log2-scale?

Mark Dunning mark.dunning at gmail.com
Thu May 21 12:44:34 CEST 2009

Hi Cei,

You can summarize on the unlogged scale by using the option log=FALSE
in createBeadSummaryData. We're still looking into the best
combination of outlier removal to use with BASH, it could be that the
Illumina method for removing outliers by a 3 MAD cut-off is still
best. This is the default option in beadarray (option

One final thing, If you plan to use VST method you'll need to
calculate detection scores prior to running VST, this can be done by:-

Detection(BSData) = calculateDetection(BSData)

The type of background correction we don't recommend is the background
subtraction performed by BeadStudio that subtracts the negative
controls from each bead-type average on an array. This causes a huge
increase in variance and missing values if you try and do a
log-transformation. However, using the combination of VST and quantile
as you plan should take care of these problems.

Hope this helps,


On Tue, May 19, 2009 at 2:25 PM, Cei Abreu-Goodger <cei at ebi.ac.uk> wrote:
> Hi Mark,
> From reading the createBeadSummaryData help page and the vignettes, I gather
> that you recommend using BASH to detect outliers, and then using "mean" in
> log2-space to summarize the data.
> If I plan to use vst/quantile to normalize my data, what would be the best
> option for processing the bead level data? I like the idea of summarizing in
> log2-space but I want a non-log-space result to use with vst. Is there a
> simple way to accomplish this?
> And while I'm asking this, I seem to remember hearing that you get better
> results without using the backgroundCorrect step. Is this recommended?
> Many thanks,
> Cei

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