Hello, I am using R 2.10.0. The sessionInfo data is below at the end of this message. I am using Ubuntu 10.04. I am attempting to re-annotate custom Affy PM-only chip using a new gene-annotation for my prokaryotic genome. I have gotten stuck on altcdfenvs, however. What I have done so far: 1. Changed the makeProbePackage code to not require MM probe data 2. Created a probe package from my probe_tab file with makeProbePackage (for some reason 4800 probes did not match between the probe_tab file and the Affy-supplied .CDF file) 3. Installed the new probe package with help from James MacDonald 4. Started following the altcdfenvs documentation....selected the constituting elemets, matched the probes.... Everything went smoothly until match analysis: > alt.cdf [[alternative HTML version deleted]]

Hi Ariel, On 6/28/2011 7:23 PM, Ariel Grostern wrote: > > > Hello, > > I am using R 2.10.0. The sessionInfo data is below at the end > of this message. I am using Ubuntu 10.04. No it isn't, as you are sending HTML to a text-only listserv and getting things chopped off. Please switch to text when sending. Best, Jim > > I am attempting to re-annotate > custom Affy PM-only chip using a new gene-annotation for my prokaryotic > genome. I have gotten stuck on altcdfenvs, however. > > What I have done so > far: > > 1. Changed the makeProbePackage code to not require MM probe data > > > 2. Created a probe package from my probe_tab file with makeProbePackage > (for some reason 4800 probes did not match between the probe_tab file and > the Affy-supplied .CDF file) > > 3. Installed the new probe package with help > from James MacDonald > > 4. Started following the altcdfenvs > documentation....selected the constituting elemets, matched the probes.... > Everything went smoothly until match analysis: > >> alt.cdf > [[alternative HTML version deleted]] > > _______________________________________________ > 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