[BioC] QCparameters for Human Exon arrays (arrayQualityMetrics)

[Gard Thomassen]

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  
website

#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