Thank you very much. Best regards, Kaj On Fri, Oct 4, 2013 at 8:03 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Kaj, > > Please don't take conversations off-list (e.g., use reply-all when > responding). > > By org package, I mean something similar to the org.Hs.eg.db package, only > for ovine instead of human. This is an organism level package, and only > does annotations pertaining to IDs that are specific to that organism > (based on Entrez Gene IDs, generally). > > Contrast that to a chip level package which maps chip IDs to various other > annotations, letting you know for instance what gene's transcript is > interrogated by a particular probe on the array. > > So, no you cannot use an org level package as annotation for a chip, > because the org package doesn't know anything about the chip IDs. That is > where the Agilent annotation file comes in. You can use that file to map > the chip IDs to Entrez Gene IDs, and then it is simple to do further > mapping on to other things you might care about (gene symbols, names, etc). > > But you won't be able to use things like nsFilter directly, as there isn't > a chip-level package that maps chip IDs to other things. Instead you will > have to 'roll your own' function. > > Best, > > Jim > > > > > On Friday, October 04, 2013 1:00:07 AM, Kaj wrote: > >> On 04/10/13 03:23, James W. MacDonald wrote: >> >>> Hi Kaj, >>> >>> Currently you cannot create a chip level annotation package without a >>> corresponding .db0 package. You can however create an organism level >>> package using makeOrgPackageFromNCBI() in the AnnotationForge >>> package, and then getting the annotation file from Agilent. You can >>> then use the Entrez Gene IDs from the annotation file to then use >>> select() to get whatever annotation you might want. >>> >>> If you are using limma, you can put the annotation data in the genes >>> slot of the MArrayLM object, and those data will appear in your >>> topTables(). >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> On Thursday, October 03, 2013 6:21:22 AM, Kaj Chokeshaiusaha [guest] >>> wrote: >>> >>>> >>>> Dear R helper, >>>> >>>> I'm trying to create the annotation package for GPL10427. It is >>>> ovine species platform, and there is no .db0 >>>> nor schema for it. >>>> >>>> I'm trying to read 'Creating an annotation package >>>> with a new database schema'. It's ashamed of me, but I'm an R >>>> beginner. I must accept that I loss most of the >>>> important contents and I cannot gather enough ideas to apply it with >>>> what I have to do. >>>> >>>> Would anyone please simplify me what I need to do in order to create >>>> the platform in this situation? >>>> >>>> With Respects, >>>> Kaj >>>> >>>> -- output of sessionInfo(): >>>> >>>> R version 3.0.2 (2013-09-25) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>>> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >>>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] hgu95av2.db_2.9.0 AnnotationForge_1.2.2 org.Hs.eg.db_2.9.0 >>>> [4] RSQLite_0.11.4 DBI_0.2-7 AnnotationDbi_1.22.6 >>>> [7] Biobase_2.20.1 BiocGenerics_0.6.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] IRanges_1.18.4 stats4_3.0.2 tcltk_3.0.2 tools_3.0.2 >>>> >>>> -- >>>> Sent via the guest posting facility at bioconductor.org. >>>> >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor@r-project.org >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: >>>> http://news.gmane.org/gmane.**science.biology.informatics.**condu ctor<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >>>> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> >> Dear Jim, >> >> Thank you very much for your answer. This can solve a lot of things. >> Would you please clarify me a bit more about the 'Organism package'? >> >> I've processed an ExpressionSet object from raw data acquired from >> this GPL10427 platform. I need to use some functions with the object; >> for example, "nsFilter" in geneFilter package. These functions ask for >> the annotation of the ExpressionSet to use all of their features. >> >> Can I set the 'Organism package' as the annotation of the ExpressionSet? >> >> Best Regards, >> Kaj >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > [[alternative HTML version deleted]]