I am trying to analyze data from Affymetrix Mouse Gene 1.0 ST arrays. I am using R 2.13.0 with affylmGUI and all its dependencies freshly installed. I have analyzed my data exactly as described in the Estrogen Worked Example from the documentation. I get no annotations on my toptable, just probeset ids. I don't see any error messages about being unable to find or download annotations, or any indication that it has tried to annotate the data at all. Reading the documentation, the only other reference to annotation that I can find points me to http://www.bioconductor.org/data/metaData.html which does not exist. How do I proceed from here?

Hi Ed, On 8/23/2011 11:42 AM, Ed Siefker wrote: > I am trying to analyze data from Affymetrix Mouse Gene 1.0 ST arrays. > I am using R 2.13.0 with affylmGUI and all its dependencies freshly > installed. I have analyzed my data exactly as described in the > Estrogen Worked Example from the documentation. > > I get no annotations on my toptable, just probeset ids. I don't see > any error messages about being unable to find or download annotations, > or any indication that it has tried to annotate the data at all. > > Reading the documentation, the only other reference to annotation that > I can find points me to http://www.bioconductor.org/data/metaData.html > which does not exist. How do I proceed from here? The ST arrays are a bit of an edge case. The affy package was never intended for this chip design, and we don't really support it like we do the 3'-biased arrays. By that I mean that we do supply cdf packages, and there is an annotation package that you can use, but the annotation package isn't named according to the rules used by the affy package, so affylmGUI isn't finding it. The package you want is called mogene10sttranscriptcluster.db (according to the naming rules for the affy package, it will likely be looking for mogene10v1st.db). I know nothing of the affylmGUI package, having never used it, so I don't know if there is an easy way to tell it that the annotation package has an unexpected name. So your recourse at this point is to play around with affylmGUI, and see if you can tell it the correct annotation package to use, or wait for Keith Satterley to respond. As the maintainer, he is most likely to know what to do. Other alternatives may be less palatable, as you evidently like a GUI interface. However, the oligo and xps packages are directly designed to work with these chips so won't have this problem. Hypothetically you could also download the source package for mogene10sttranscriptcluster.db, rename things to coincide with what affylmGUI is expecting, build and install. But if you are going to do that, you might as well save time and energy by just switching to command-line based packages that are more amenable to working with this chip. Best, Jim > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

Ed, I know what I am about to suggest soundds awkward but you can donwload the annotation from the affy web site, sort your outout by accesion #s and paste in the annotation aligned by accession number and then resort by p-value. With hopes that the above helps, Rich On Tue, 23 Aug 2011, Ed Siefker wrote: > I am trying to analyze data from Affymetrix Mouse Gene 1.0 ST arrays. > I am using R 2.13.0 with affylmGUI and all its dependencies freshly > installed. I have analyzed my data exactly as described in the > Estrogen Worked Example from the documentation. > > I get no annotations on my toptable, just probeset ids. I don't see > any error messages about being unable to find or download annotations, > or any indication that it has tried to annotate the data at all. > > Reading the documentation, the only other reference to annotation that > I can find points me to http://www.bioconductor.org/data/metaData.html > which does not exist. How do I proceed from here? > > _______________________________________________ > 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 > > -- ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist Herbert Irving Comprehensive Cancer Center Biomedical Informatics Shared Resource Lecturer Department of Biomedical Informatics Box 95, Room 130BB or P&S 1-420C Columbia University Medical Center 630 W. 168th St. New York, NY 10032 (212)305-6901 (5-6901) (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "The last 250 pages of the last Harry Potter book took place in one day because alot happened in that day. All of Ulysses takes place in one day and nothing happened in that day." -Rose Friedman, age 11