[BioC] QC question using simpleaffy

Laurent Gatto L.Gatto at dnavision.be
Tue Jun 26 12:12:00 CEST 2007

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. 



Laurent Gatto

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of James
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 at bioBCalls == "A"), they are not fully consistent with the
arrays with the lowest qc at 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,


The fish are biting.

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