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 -- --------------------------------------------------------------- The robbed that smiles, steals something from the thief. - Shakespeare --------------------------------------------------------------- [[alternative HTML version deleted]]

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, amit mandal Graduate student Genomics & Molecular Medicine Lab IGIB Delhi -- --------------------------------------------------------------- The robbed that smiles, steals something from the thief. - Shakespeare --------------------------------------------------------------- [[alternative HTML version deleted]]