Hi Anja, It looks like meeboQuality couldn't find the controls identifiers. This function is looking for MEEBO ids starting with mMC, mCT, mCP... Does your image processing output file include them? If so, did you try to specify the name of your column containing the MEEBO identifier in the arguments of the function? Regards, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Anja Schiel Sent: Fri 3/31/2006 4:51 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] MEEBO-tool in arrayQuality Hello, I am running the newest version of arrayQuality (1.6.3) to analyse MEEBO arrays. We have spotted the library on two slides and I would like to use the very nice new meebo-tool from the package. I get as far as making the diagnostic plot, but seem to be unable to use the mismatch controls or get the plots with the spike in ratios (I have adapted the Spike in file, I only used Ambion Spikes). This is my session output, in R 2.2.0, Linux, package 1.6.3. Can anybody give me a hint what seems to go wrong with the NA at the end? test<-meeboQuality(SpikeTypeFile="AmbionA.txt", cy3col="MassCY3",cy5col="MassCY5", namecol="Name") [1] "Staring meeboQuality" Read ./AS240605_1.gpr [1] "Starting meeboQualityPlots" [1] TRUE [1] TRUE [1] TRUE save as diagPlot.AS240605_1.png Error: subscript out of bounds Error in plot(as.numeric(ctl[mma, "NumberMM"]) * 100/70, mnorm $A[as.vector(ctl[mma, : unable to find the argument 'y' in selecting a method for function 'NA' > Thanks, Anja A. Schiel, Ph.D. Department of Human Genetics Leiden University Medical Center Room T-03-054 phone: 071 - 526 9472 fax: 071 - 526 8275 visiting address: Einthovenweg 20, Leiden postal address: LUMC Post zone S-4-P PO Box 9600 2300 RC Leiden [[alternative HTML version deleted]] _______________________________________________ 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