[BioC] QCparameters for Human Exon arrays (arrayQualityMetrics)

Audrey Kauffmann audrey at ebi.ac.uk
Thu Nov 26 12:10:47 CET 2009

Hi Gard,

Sorry for the delay answering. I do not have much experience using
arrayQualityMetrics for Exon arrays, so I have talked with Crispin Miller
(simpleaffy package) about it and according to him "most of the Affymetrix
QC metrics for the 3' IVT arrays aren't directly applicable to the exon
arrays. They rely on MAS 5 and paired MM spots (neither of which are
applicable for exon arrays) and also make assumptions on 3'/5' ratios that
don't apply because the exon array chemistry is different."
I have now modified the package and version 2.4.3 of arrayQualityMetrics
should not perform the QC statistics from simpleaffy when "exon" is in the

Best wishes,

> Hi.
> I am trying to get the arrayQualityMetrics package to run on a set of
CEL files from the Human Exon array from Affymetrix
> My problems begin when I want to run the arrayQualityMetrics function
and it gives the following error message :
> running R 2.9.2 and bioconductor version 2.4
>  >library(affy)
>  >library(simpleaffy)
>  >ibrary(arrayQualityMetrics)
>  >ecesbatch<-read.affybatch("H1.CEL", "H2.CEL", "H3.CEL", "H4.CEL",
> "H5.CEL", "H6.CEL", "H7.CEL", "H8.CEL", "H9.CEL", "H10.CEL",
> "H11.CEL", "H12.CEL", "H13.CEL", "H14.CEL", "H15.CEL", "H16.CEL")
> ## attach cdf to expr set
> ecesbatch at cdfName <- "exon.pmcdf" ## this is a cdf file from the XMAP
> #Check the name is correct for the cdf file (unneccessary)
>  > cdfname <- cleancdfname(cdfName(ecesbatch))
>  > cdfname
> [1] "exon.pmcdf"
>  >arrayQualityMetrics(expressionset = ecesbatch,outdir =
> "output",force = TRUE,do.logtransform = TRUE)
> This cmd runs for a very long time and generates a bunch of .pdfs and
.pngs and an empty QCReport.html file.
> And R says there is an error sonce the arrayQualityMetrics package does
not know the QCparameters of this chip.
> I have found an instruction from C. Miller (one of the persons behind
simpleaffy) about how use the three functions provided by the
> simpleaffy package, or to make the needed .qcdf file:
> I need alpha values (that is okay) and I need control and spike
> probeIDs.
> I am using the Human Exon array 1.0 from affymetrix, and I do not know
what to fill in in the .qcdf file,
> anyone who knows how to get by this problem?
> Trying to get the probenames to set the values I ran into another problem..
>  > prbs <- ls(cdfname)
> Error in as.environment(pos) :
>    no item called "exon.pmcdf" on the search list
>  >
> crashes like this shown here.
> Please if anyone knows or has an idea, basicly what I need is
> the .qcdf file for the HUman Exon array from Affy.
> Best regards
> Gard
> #################################
> Gard Thomassen
> Ph.D student CMBN, Rikshospitalet, Oslo
> Bioinformatician, Radiumhospitalet, Oslo
> Norway
> Email : gardt at ifi.uio.no
> Office: + 47 22781736
> Phone +47 93674926
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