
The background correction part of lumi package is still not well developed.
We suppose the data had already been background-corrected by BeadStudio. As
a result, we usually do not do background correction in the preprocessing. (
The forcePositve method basically adds an offset to avoid NA in log2
transform.) If you really concern about background removal, you can take a
look of beadarray package, which provides bead level preprocessing methods.

The manuscript is still under review. But we added the evaluation vignette
in the recent version. Pls check the Bioconductor developing website I sent
you yesterday.

Pan


On 8/28/07 7:57 AM, "Ingrid H. G. Østensen"
<Ingrid.H.G.Ostensen@rr-research.no> wrote:

> 
> After reading different documents I found I have come to a conclusion:
> The first part does not work because forecePositice does not make the
> expression values to much bigger than zero, and log (in vst) is taken of a
> negative number. If I use bg.adjust the values are not that close to zero and
> vst (and log2) works fine. Can this be correct? Can I use the one that works
> or can it be other errors that make this happen and the data not to be
> trusted?
> 
> Alice gave me some help understanding the increasing number of genes, but does
> anyone have more detailes?
> 
> And where can I find the articles mentioned to in the lumi vignette?
> 
> I also tried to use R 2.6.0 and the new version of lumi but that did not work
> for this file or other files that do work.
> 
> Regards,
> Ingrid
> 
> 


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