michael watson (IAH-C) wrote: > I am sure Marc would be very accomodating :) > > What would be excellent, however, is if I could create a db0 package > myself. > I have all the data - all the links from ensembl, entrez, GO, KEGG, > Unigene etc. > > Is it planned to provide tools to create db0 packages? My understanding is that this is part of the plan. Marc would know better, and will also have a better idea of the timeline for such tools to appear. > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: 29 August 2008 15:50 > To: michael watson (IAH-C) > Cc: Sean Davis; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] GO over representation analysis > > michael watson (IAH-C) wrote: >> OK, so there is not chicken.db0 or cow.db0 package so that rules that >> one out. > > Really? Does this mean you contacted Marc Carlson about creating > packages for these species and he told you it was out of the question? I > > would find that rather surprising. In the past (and a quick search of > the BioC listserv bears this out), he has been rather accommodating. > >> My experience is that most people have a "star" schema of information >> linking probes to genes to GO IDs, Pathways, Entrez etc etc. >> >> It *should* be simple to make an annotation package out of this, but > it >> isn't. >> >> And I hate to be hper-critical but the Vignette for AnnBuilder is >> virtually inaccessible... > > Yes, well it is a bit much to ask that the vignette for a soon to be > deprecated package be updated, no? > >> -----Original Message----- >> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] >> Sent: 29 August 2008 14:07 >> To: Sean Davis >> Cc: michael watson (IAH-C); bioconductor at stat.math.ethz.ch >> Subject: Re: [BioC] GO over representation analysis >> >> There is one slight additional wrinkle. AnnotationDbi currently > supports >> fewer species than AnnBuilder. Building a package using AnnotationDbi > is >> (at least) a two step process, of which only one is required of the > end >> user. The first step(s) are to build a database containing all > relevant >> data for a given species that is then used to populate the > chip-specific >> package databases. >> >> If you are interested in an annotation package that is not yet > supported >> by AnnotationDbi, then you will need to consult with Marc Carlson to > get >> the primary database built. >> >> Best, >> >> Jim >> >> >> >> Sean Davis wrote: >>> On Fri, Aug 29, 2008 at 8:33 AM, michael watson (IAH-C) >>> <michael.watson at="" bbsrc.ac.uk=""> wrote: >>>> Dear All >>>> >>>> I think one thing that is frustrating here is that there is not a >> simple >>>> guide here for people who want to create an annotation package for > an >>>> array that does not yet have one. >>>> >>>> Do we use AnnotationDbi? Or AnnBuilder? Or is there another way? >>>> >>>> What is the "best practice" for building an annotation package? >>> Hi, Mick. The confusion arises because annotation packages have been >>> migrated from the environment-based packages built by AnnBuilder to >>> the newer SQLite-based packages of AnnotationDbi. The answer depends >>> on which version of R and, therefore, which version of Bioconductor >>> you are using. That said, the standard for the current and future >>> releases (for the near-future, anyway) is to use SQLForge from >>> AnnotationDbi. >>> >>> Sean >>> >>>> -----Original Message----- >>>> From: bioconductor-bounces at stat.math.ethz.ch >>>> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Marc >>>> Carlson >>>> Sent: 25 August 2008 17:03 >>>> To: Heike Pospisil >>>> Cc: bioconductor at stat.math.ethz.ch >>>> Subject: Re: [BioC] GO over representation analysis >>>> >>>> You could just make an annotation package for the array in question >> by >>>> using the SQLForge code in the AnotationDbi package. >>>> You can find instructions on how to do this here: >>>> >>>> > http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html >>>> Let me know if you have any questions about SQLForge. >>>> >>>> >>>> Marc >>>> >>>> >>>> >>>> Heike Pospisil wrote: >>>>> Hello Bioconductors, >>>>> >>>>> I am looking for a method to perfom over representation analysis >> (Gene >>>>> Ontology) within R. I have data from the Maize Oligonucleotide > Array >>>> (two >>>>> channel) with the GO categories for all probes on this array. I > have >>>>> clustered the genes using Maanova and I am interested in GO over >>>>> representation of the gene lists from these clusters. >>>>> >>>>> I know the GO tools from Bioconductor (e.g. GOstats), but I do not >>>> know how to >>>>> adapt the analysis to an 'unusual' array with no annotation data >>>> package and >>>>> now Entrez IDs. Any hints? >>>>> >>>>> Thanks in advance, >>>>> Heike >>>>> >>>> _______________________________________________ >>>> 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 >>> _______________________________________________ >>> 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 48109-0646 734-936-8662