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

Cei Abreu-Goodger cei at ebi.ac.uk
Tue May 19 15:25:06 CEST 2009

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 

Many thanks,


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