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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