I've gotten arrayQualityMetrics to work with an ExpressionSet, i.e. post-processed data, but can't get it to work with pre-processed data because I cannot make an affyBatch from the new Affy Rat Gene ST arrays. Affy puts out a .qcc file but not a qcdef file for these arrays. I would like to be able to look at pre-processed QA. Also, I miss some of the features of affyQAReport such as Nuse plots, which have been very helpful to me in identifying problem arrays. Any suggestions? Mark Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** On Tue, Oct 14, 2008 at 12:07 PM, Robert Gentleman <rgentlem@fhcrc.org>wrote: > My efforts now are in support of Audrey Kauffmann's arrayQualityMetrics > package, which provide much more comprehensive support for QA on > microarrays. Have you tried it? > > best wishes > Robert > > > Mark Kimpel wrote: > >> I've become quite fond of affyQAReport and have numerous examples of cases >> where I have used it to help identify problem arrays that my core >> facility, >> which uses only Affymetrix tools, have said are fine. I am now using the >> Affy Rat Gene 1.0 ST array and apparently cannot convert it into an >> affyBatch (required as input to affyQAReport) using the packages I have >> been >> steered to for analysis (oligo and pdInfoBuilder) . Is there another >> package >> or approach one can use to do QA on these newer chips? I did try hacking >> affyQAReport, but ran into my own limitations when I got to the function >> qc, >> which sets a cdf environment variable. >> >> Mark >> ------------------------------------------------------------ >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 399-1219 Home >> Skype: mkimpel >> >> "The real problem is not whether machines think but whether men do." -- B. >> F. Skinner >> ****************************************************************** >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem@fhcrc.org > [[alternative HTML version deleted]]