Dear Mark, Thank you. I don't have access to the source tree. Does this mean that I need to download the annotate library again, or can I grab the functions separately? If the latter, how is that done? Best, Monnie Monnie McGee, Ph.D. Associate Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035 -----Original Message----- From: Marc Carlson [mailto:mcarlson@fhcrc.org] Sent: Wed 10/8/2008 11:03 AM To: McGee, Monnie Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0 Hi Monnie, These functions seem to have disappeared as we moved from the older annotations to the new kind. I have just checked in some replacement functions for you into the development branch (entrezGeneByID() and entrezGeneQuery()). If you have access to the source tree then these are already available, but they should be on the website within 24 hours. Marc McGee, Monnie wrote: > Dear List, > > I was going through the examples in the query documentation (written in June of 2008) for the annotate package when I came to an error. The function "locuslinkQuery" no longer seems to exist, and neither does "locuslinkByID". Here are my code and session info: > > >> sessionInfo() >> > R version 2.7.2 (2008-08-25) > powerpc-apple-darwin8.11.1 > > locale: > C > > attached base packages: > [1] splines tools stats graphics grDevices > [6] utils datasets methods base > > other attached packages: > [1] XML_1.96-0 cMAP_1.15.1 > [3] GOstats_2.6.0 Category_2.6.0 > [5] genefilter_1.20.0 survival_2.34-1 > [7] RBGL_1.16.0 annotate_1.18.0 > [9] xtable_1.5-3 GO.db_2.2.0 > [11] hgu133a_2.2.0 RbcBook1_1.8.0 > [13] graph_1.18.1 KEGG_2.2.0 > [15] hgu95av2.db_2.2.0 AnnotationDbi_1.2.1 > [17] RSQLite_0.6-8 DBI_0.2-4 > [19] Biobase_2.0.1 hgu95av2_2.2.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.11 > > >> locuslinkQuery("leukemia","Hs") >> > Error: could not find function "locuslinkQuery" > > The annotate package is attached, as are BioBase and XML, which are the packages that the documentation states are needed. I noticed that the session info for the documenation had XML version 1.95.2 instead of 1.96-0 as in mine. I also listed all of the functions available in the annotate package, using ls(package:annotate) and locuslinkQuery is not there. I looked around for various substitutes, but I could not find any. Has this function been removed? If so, what is its replacement? If not, what did I do wrong? > > I also searched the help archives, but did not find any reference to this problem. > > By the way, right now I have to set my locale to "C" every time I start R. Is there a way to make this automatic? > > Thanks, > Monnie > > Monnie McGee, Ph.D. > Associate Professor > Department of Statistical Science > Southern Methodist University > Ph: 214-768-2462 > Fax: 214-768-4035 > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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

Hi Monnie, You will need to run the 1.19.3 version of the annotate package. http://www.bioconductor.org/packages/2.3/bioc/html/annotate.html Marc McGee, Monnie wrote: > Dear Mark, > > Thank you. > > I don't have access to the source tree. Does this mean that I need to download the annotate library again, or can I grab the functions separately? If the latter, how is that done? > > Best, > Monnie > > Monnie McGee, Ph.D. > Associate Professor > Department of Statistical Science > Southern Methodist University > Ph: 214-768-2462 > Fax: 214-768-4035 > > > > -----Original Message----- > From: Marc Carlson [mailto:mcarlson at fhcrc.org] > Sent: Wed 10/8/2008 11:03 AM > To: McGee, Monnie > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] Missing function locuslinkQuery and locuslinkBYID in annotate 1.18.0 > > Hi Monnie, > > These functions seem to have disappeared as we moved from the older > annotations to the new kind. I have just checked in some replacement > functions for you into the development branch (entrezGeneByID() and > entrezGeneQuery()). If you have access to the source tree then these > are already available, but they should be on the website within 24 hours. > > Marc > > > > McGee, Monnie wrote: > >> Dear List, >> >> I was going through the examples in the query documentation (written in June of 2008) for the annotate package when I came to an error. The function "locuslinkQuery" no longer seems to exist, and neither does "locuslinkByID". Here are my code and session info: >> >> >> >>> sessionInfo() >>> >>> >> R version 2.7.2 (2008-08-25) >> powerpc-apple-darwin8.11.1 >> >> locale: >> C >> >> attached base packages: >> [1] splines tools stats graphics grDevices >> [6] utils datasets methods base >> >> other attached packages: >> [1] XML_1.96-0 cMAP_1.15.1 >> [3] GOstats_2.6.0 Category_2.6.0 >> [5] genefilter_1.20.0 survival_2.34-1 >> [7] RBGL_1.16.0 annotate_1.18.0 >> [9] xtable_1.5-3 GO.db_2.2.0 >> [11] hgu133a_2.2.0 RbcBook1_1.8.0 >> [13] graph_1.18.1 KEGG_2.2.0 >> [15] hgu95av2.db_2.2.0 AnnotationDbi_1.2.1 >> [17] RSQLite_0.6-8 DBI_0.2-4 >> [19] Biobase_2.0.1 hgu95av2_2.2.0 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.11 >> >> >> >>> locuslinkQuery("leukemia","Hs") >>> >>> >> Error: could not find function "locuslinkQuery" >> >> The annotate package is attached, as are BioBase and XML, which are the packages that the documentation states are needed. I noticed that the session info for the documenation had XML version 1.95.2 instead of 1.96-0 as in mine. I also listed all of the functions available in the annotate package, using ls(package:annotate) and locuslinkQuery is not there. I looked around for various substitutes, but I could not find any. Has this function been removed? If so, what is its replacement? If not, what did I do wrong? >> >> I also searched the help archives, but did not find any reference to this problem. >> >> By the way, right now I have to set my locale to "C" every time I start R. Is there a way to make this automatic? >> >> Thanks, >> Monnie >> >> Monnie McGee, Ph.D. >> Associate Professor >> Department of Statistical Science >> Southern Methodist University >> Ph: 214-768-2462 >> Fax: 214-768-4035 >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> 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 >> > > > >

> Dear Mark, > > Thank you. > > I don't have access to the source tree. Does this mean that I need to download the annotate library again, or can I grab the functions separately? If the latter, how is that done? Everyone has access to the source tree. See the "Developer Page" "svn repository" link. However, you would *never* get the revised functions separately. Always use biocLite to install or reinstall revised software as *packages*. To get the devel branch versions, you need to be working from a devel version of R (2.9 at this time).

Hi Monnie, McGee, Monnie wrote: > Dear Mark, > > Thank you. > > I don't have access to the source tree. Does this mean that I need > to download the annotate library again, or can I grab the functions > separately? If the latter, how is that done? You don't want to grab the functions separately. Just re-install using biocLite(), assuming the changes Marc made have propagated to the download server by now. Best, Jim > > Best, Monnie > > Monnie McGee, Ph.D. Associate Professor Department of Statistical > Science Southern Methodist University Ph: 214-768-2462 Fax: > 214-768-4035 > > > > -----Original Message----- From: Marc Carlson > [mailto:mcarlson at fhcrc.org] Sent: Wed 10/8/2008 11:03 AM To: McGee, > Monnie Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Missing > function locuslinkQuery and locuslinkBYID in annotate 1.18.0 > > Hi Monnie, > > These functions seem to have disappeared as we moved from the older > annotations to the new kind. I have just checked in some replacement > functions for you into the development branch (entrezGeneByID() and > entrezGeneQuery()). If you have access to the source tree then these > are already available, but they should be on the website within 24 > hours. > > Marc > > > > McGee, Monnie wrote: >> Dear List, >> >> I was going through the examples in the query documentation >> (written in June of 2008) for the annotate package when I came to >> an error. The function "locuslinkQuery" no longer seems to exist, >> and neither does "locuslinkByID". Here are my code and session >> info: >> >> >>> sessionInfo() >>> >> R version 2.7.2 (2008-08-25) powerpc-apple-darwin8.11.1 >> >> locale: C >> >> attached base packages: [1] splines tools stats graphics >> grDevices [6] utils datasets methods base >> >> other attached packages: [1] XML_1.96-0 cMAP_1.15.1 >> [3] GOstats_2.6.0 Category_2.6.0 [5] genefilter_1.20.0 >> survival_2.34-1 [7] RBGL_1.16.0 annotate_1.18.0 [9] >> xtable_1.5-3 GO.db_2.2.0 [11] hgu133a_2.2.0 >> RbcBook1_1.8.0 [13] graph_1.18.1 KEGG_2.2.0 [15] >> hgu95av2.db_2.2.0 AnnotationDbi_1.2.1 [17] RSQLite_0.6-8 >> DBI_0.2-4 [19] Biobase_2.0.1 hgu95av2_2.2.0 >> >> loaded via a namespace (and not attached): [1] cluster_1.11.11 >> >> >>> locuslinkQuery("leukemia","Hs") >>> >> Error: could not find function "locuslinkQuery" >> >> The annotate package is attached, as are BioBase and XML, which are >> the packages that the documentation states are needed. I noticed >> that the session info for the documenation had XML version 1.95.2 >> instead of 1.96-0 as in mine. I also listed all of the functions >> available in the annotate package, using ls(package:annotate) and >> locuslinkQuery is not there. I looked around for various >> substitutes, but I could not find any. Has this function been >> removed? If so, what is its replacement? If not, what did I do >> wrong? >> >> I also searched the help archives, but did not find any reference >> to this problem. >> >> By the way, right now I have to set my locale to "C" every time I >> start R. Is there a way to make this automatic? >> >> Thanks, Monnie >> >> Monnie McGee, Ph.D. Associate Professor Department of Statistical >> Science Southern Methodist University Ph: 214-768-2462 Fax: >> 214-768-4035 >> >> ------------------------------------------------------------------- ----- >> >> >> _______________________________________________ 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 > > _______________________________________________ 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 Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-5646 734-936-8662