Hi Konika, On Wed, Mar 20, 2013 at 5:18 AM, konika chawla <chawla at="" bio.ntnu.no=""> wrote: > Hi > Sorry I could get back to this before > Here is my sessionInfo() > R version 2.13.0 (2011-04-13) As you can see, your version of R is 2 years old, and the bioconductor packages being installed are similarly ~ 2 years old (looks like it's bioc version 2.8). You should update your R to the latest (2.15.3) and reinstall your packages via `biocLite`. You will get the newer packages. HTH, -steve -- Steve Lianoglou Defender of The Thesis | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Hi Konica, Your locally installed version of GO.db is from a couple of years ago. We have actually updated it many times since then. The newest version is 2.9.0 for devel (or 2.8.0 if you are using the release). You can get an update by just using the following command: source("http://bioconductor.org/biocLite.R")|| biocLite("GO.db") If you have questions about how to use biocLite(), please see our web site here: http://www.bioconductor.org/install/ Marc On 03/20/2013 02:18 AM, konika chawla wrote: > Hi > Sorry I could get back to this before > Here is my sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] GO.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 > [4] AnnotationDbi_1.14.1 Biobase_2.12.2 biomaRt_2.8.1 > [7] gregmisc_2.1.1 gplots_2.8.0 caTools_1.12 > [10] bitops_1.0-4.1 gtools_2.6.2 gmodels_2.15.1 > [13] gdata_2.8.2 > > loaded via a namespace (and not attached): > [1] MASS_7.3-14 RCurl_1.6-10 XML_3.95-0 > > > > Thanks for any suggestions... > Konika > > > From: Marc Carlson < mcarlson@... > <http: gmane.org="" get-address.php?address="mcarlson%2dq9hIisBwmLrYtjv" yw6ydsg%40public.gmane.org=""> > > > Subject: Re: Is GO.db out of date? > <http: news.gmane.org="" find-="" root.php?message_id="%3c51422CDC.4080402%40fhcrc.org%3e"> > Newsgroups: gmane.science.biology.informatics.conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > Date: 2013-03-14 20:02:36 GMT (5 days, 13 hours and 12 minutes ago) > Hi Konika, > > In order to answer your question, I need to know which version of GO.db > you are using. Can you please provide the results from your sessionInfo() ? > > GO.db is updated with every release. So the current release was updated > last fall. The version in the development branch (which will become the > release in a couple weeks), was updated last week. > > Marc > > On 03/14/2013 05:58 AM, konika chawla wrote: > > Hi > > I am using GO.db package for finding GO terms for a given Id. > > I failed to find few of these for example : GO:0001200, GO:0001227, GO:0001228 > > I used the code : > > goterms<-unlist(eapply(GOTERM,function(x) x<at> Term)) > > goterms<-as.matrix(goterms) > > which(rownames(goterms)=="GO:0001200") > >> integer(0) > > In The gene Ontology database "GO:0001200" is for "metal ion regulated sequence-specific DNA binding > RNA polymerase II transcription factor activity". > > I also found that GOA has 39117 GO terms while GO.db has 32255 GO terms. I checked the reference manual for > GO.db which says it is updated biannually but the last update is of April2012. > > I am wondering if it will be updated soon else please suggest any other package which has similar functionality. > > Or is there any error in the code ?? > > Thanks > > Konika Chawla > > PhD Student > > Department of Biology > > NTNU > > > > > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@... <http: gmane.org="" get-address.php?address="Bioco" nductor%2d0bnbq1pawb4bxfe83j6qeq%40public.gmane.org=""> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives:http://news.gmane.org/gmane.science.biology.i nformatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@... <http: gmane.org="" get-address.php?address="Biocondu" ctor%2d0bnbq1pawb4bxfe83j6qeq%40public.gmane.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives:http://news.gmane.org/gmane.science.biology.info rmatics.conductor > > Konika Chawla > PhD Student > Department of Biology > NTNU > > > > [[alternative HTML version deleted]]