Dear all, I am using the beadarray package to analyze my Illumina beadarray data. At the moment I have some problems with using the readBeadSummaryData function. I tried to find the problem by looking closer at the function. Than I noticed that the readQC function is not present in the version 2.2.0 of beadarray whereas it still part of the readBeadSummaryData. So in my obtained ExpressionSetIllumina object no QC information is present. Has anyone noticed this as well? Is there a newer version op the package available which I should use? Thanks in advance. Best regards, Susan

Hi Susan, The readQC function is still present in version 2.2.0, but it is called from within readBeadSummaryData rather than being called directly by the user. The fact that you have no QC information in your ExpressionSetIllumina data object could be to do with the format of your QC data. You should check that the qc.sep, qc.skip and qc.columns arguments are correct. Do you get any warning or error messages when running readBeadSummaryData? Regards, Mark On Thu, Jul 7, 2011 at 3:58 PM, Susan <susan.coort at="" maastrichtuniversity.nl=""> wrote: > Dear all, > > I am using the beadarray package to analyze my Illumina beadarray data. At the > moment I have some problems with using the readBeadSummaryData function. I tried > to find the problem by looking closer at the function. Than I noticed that the > readQC function is not present in the version 2.2.0 of beadarray whereas it > still part of the readBeadSummaryData. So in my obtained ExpressionSetIllumina > object no QC information is present. Has anyone noticed this as well? Is there a > newer version op the package available which I should use? Thanks in advance. > > Best regards, > Susan > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >