hello all,
    I've a query regarding the arguments being passed for the *lumiB*command.
                     I'm working with *Illumina WG-6 v3* datasets and I want
to replicate the exact background correction effect as done by BeadStudio (*v.
3.1.3.0*). I've *imported out non-bkg corrected, non-normalized data* from
BeadStudio and doing the analysis using *lumi*.
     I'm unable to understand well how the optional *probs* argument is
working in lumiB. E.g.

 lumi.B <- lumiB(example.lumi, method='bgAdjust', probs=0)  # from lumiB
help page

If one is not passing the *probs* argument, then what value is taken by
default; and what value should be passed for the same if an exact effect of
the BeadStudion bkg correction is desired. When I did bkg correction using
BeadStudio, I landed with many negative values (in thousands). But here when
I used *lumiB* with default settings,

nuc.lumi.B<-lumiB(nuc.lumi,method='bgAdjust',verbose=TRUE)  # used code

I don't find any resulting negative values.
Kindly help; where could I have done the discrepancy?


thanks n' regards,


--
Graduate Student
Genomics & Molecular Medicine Unit
Institute of Genomics & Integrative Biology (IGIB)
Delhi

-- 
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The robbed that smiles, steals something
from the thief.
- Shakespeare
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