Laurent,

Yeah, I figured this out later. They are different. So in terms of identifying outliers by percentage of present calls, would that be reasonable to just pick up those with lowest percentage of present calls? The manual says that the
absolute value of percent.present is not a good metric, since some cells
naturally express more genes than others, then is there any other way to take into consideration of this? 

Thanks,
James

Laurent Gatto <L.Gatto@dnavision.be> wrote: Dear James,

bioBCalls tells if the bioB probe (one hybridization control probe,
AFFX-BioB-3_at or AFFX-r2-Ec-bioB-3_at depending on the array type) is
present whereas is percent.present gives the percentage of all probe
sets that are called present on the array. 

HTH,

Laurent

Laurent Gatto
DNAVISION SA

-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of James
Anderson
Sent: Monday, June 25, 2007 9:05 PM
To: bioconductor
Subject: [BioC] QC question using simpleaffy

I read from the manual of QC using simpleaffy, the object obtained is
called "qc", which I type 
slotNames (qc)

[1] "scale.factors"      "target"             "percent.present"   
[4] "average.background" "minimum.background" "maximum.background"
[7] "spikes"             "qc.probes"          "bioBCalls"        

I am trying to locate those arrays with some quality problem.
when I type
which(qc@bioBCalls == "A"), they are not fully consistent with the
arrays with the lowest qc@percent.present. The manual says that the
absolute value of percent.present is not a good metric, since some cells
naturally express more genes than others. So what's the other
information except percent.present that is used to determine whether an
array is "A" or "P"? 

Many thanks,

James


 
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