Dear all, Having an error message come up when trying to use qc on my bovine affy genechips "Error in setQCEnvironment(cdfn) : Could not find array definition file ' bovinecdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually." I doubled checked that I had uploaded the latest bovinecdf package (2.0.0 versus 1.4.8 version) but neither solves the issue. I know I can set the file myself using cdfName and cleancdfname but need to know where I go to doublecheck that I have the right values for the alphas and controls? Any help would be apprecaited. I am new to this and still figuring it all out. Thanks Louisa Rispoli "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein

Hi Louisa, Louisa A Rispoli/AS/EXP/UTIA wrote: > Dear all, > > Having an error message come up when trying to use qc on my bovine affy > genechips > > "Error in setQCEnvironment(cdfn) : > Could not find array definition file ' bovinecdf.qcdef '. Simpleaffy does > not know the QC parameters for this array type. > See the package vignette for details about how to specify QC parameters > manually." > > I doubled checked that I had uploaded the latest bovinecdf package (2.0.0 > versus 1.4.8 version) but neither solves the issue. I know I can set the > file myself using cdfName and cleancdfname but need to know where I go to > doublecheck that I have the right values for the alphas and controls? Not sure about the alphas - it seems like (0.05, 0.065) are common to use. For the controls, look at the last two pages of the simpleaffy vignette. You need the AFFX probeset IDs that correspond to these spike in and control probesets. You can look for them using e.g., prbs <- ls(bovinecdf) affxprbs <- prbs[grep("AFFX", prbs)] then look at affxprbs to see which ones correspond to what you see in the back of the simpleaffy vignette. Next, see http://article.gmane.org/gmane.science.biology.informatics.conductor/1 4298/match=qc+parameter for how to get set up. Best, Jim > > Any help would be apprecaited. I am new to this and still figuring it all > out. > > Thanks > > Louisa Rispoli > > > "If we knew what we were doing, it wouldn't be called Research." - Albert > Einstein > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623