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

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 cdfname. Best wishes, Audrey > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >