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

[Mark Dunning]

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
method="Illumina").

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,

Mark

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
>