hi, i wanted to build an annotation package for the Affymetrix rat2302 chip. because i have problems to access ftp servers through the http_proxy i am behind (it works perfectly with http, but not through the ftp protocol) i downloaded the LocusLink and UniGene database files and created my UG and LL objects with the option "fromWeb=FALSE". i supposed that it would work, but i got an error "could not open connection to ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.info". i supposed the function would not try to establish connections to the internet when i submit the attribute fromWeb=FALSE and define a local url beginning with file:// . maybe this is a bug, it may be better if one can submit also the url of a local info file to get the information about the built that was used... i wrote a wrapper function that overwrites the getUGBuilt() function to read a local info file, but it took me some time to understand why the call everytime failed another question: locuslink has been substituted by the Gene database... are there plans that AnnBuilder will annotate using the new database? thanks, jo

Hi Jo, "Dipl.-Ing. Johannes Rainer" <johannes.rainer@tugraz.at> writes: > i wanted to build an annotation package for the Affymetrix rat2302 > chip. because i have problems to access ftp servers through the > http_proxy i am behind (it works perfectly with http, but not through > the ftp protocol) i downloaded the LocusLink and UniGene database > files and created my UG and LL objects with the option > "fromWeb=FALSE". i supposed that it would work, but i got an error > "could not open connection to > ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.info". i supposed the > function would not try to establish connections to the internet when i > submit the attribute fromWeb=FALSE and define a local url beginning > with file:// . maybe this is a bug, We will look into this. > another question: locuslink has been substituted by the Gene > database... are there plans that AnnBuilder will annotate using the > new database? Yes, we are actively working on this and expect to have something very soon. Best, + seth

>i wanted to build an annotation package for the Affymetrix rat2302 >chip. because i have problems to access ftp servers through the >http_proxy i am behind (it works perfectly with http, but not through >the ftp protocol) i downloaded the LocusLink and UniGene database files >and created my UG and LL objects with the option "fromWeb=FALSE". i >supposed that it would work, but i got an error "could not open >connection to ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.info". i >supposed the function would not try to establish connections to the >internet when i submit the attribute fromWeb=FALSE and define a local >url beginning with file:// . maybe this is a bug, it may be better if >one can submit also the url of a local info file to get the information >about the built that was used... i wrote a wrapper function that >overwrites the getUGBuilt() function to read a local info file, but it >took me some time to understand why the call everytime failed The code was trying to get the build information. Each of the objects (e. g. LL, UG, ...) has to be provided with a value for built to completely turn off the connection). We will try to figure out a better way of handling this. Thanks. > >another question: locuslink has been substituted by the Gene >database... are there plans that AnnBuilder will annotate using the new >database? > >thanks, jo > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

this sounds nice! i will try it and report the outcome to you, thanks, jo Quoting Steffen Durinck <sdurinck@ebi.ac.uk>: > Hi, > > If you want, you could also try out the biomaRt package see > developmental packages. biomaRt retrieves its annotation via direct > mysql queries to Ensembl. I don't know if that goes through your > firewall... > rat2302 is present in Ensembl so you could query that for annotation > such as gene information, go, sequence,snp,... Ensembl also has > entrez-gene id's (in the package they are still called locuslink but > in the database they are already entrez-gene). > This package is still in an early phase so if you decide to use it > and have any comments, those would be very helpful for directing > further development. > > Below an example for rat230_2.. > > Cheers, > Steffen > > >library(biomaRt) > > mart<-martConnect() > - Connected to ensembl_mart_29, ensembl_mart_29, ensembl_mart_29 and > ensembl_mart_29 - > > > getGene(id="1370752_a_at",array="rat230_2",mart=mart) > An object of class "martTable" > Slot "id": > [1] "1370752_a_at" > > Slot "table": > $symbol > [1] "P53_RAT" > > $description > [1] "CELLULAR TUMOR ANTIGEN P53 (TUMOR SUPPRESSOR P53). > [Source:SWISSPROT;Acc:P10361]" > > $band > [1] "q24" > > $chromosome > [1] "10" > > $start > [1] 56420181 > > $end > [1] 56424324 > > > getGO(id="1370752_a_at",array="rat230_2",mart=mart) > An object of class "martTable" > Slot "id": > [1] "1370752_a_at" "1370752_a_at" "1370752_a_at" "1370752_a_at" > "1370752_a_at" > [6] "1370752_a_at" "1370752_a_at" > > Slot "table": > $GOID > [1] "GO:0003700" "GO:0005634" "GO:0006350" "GO:0006355" "GO:0006915" > [6] "GO:0045786" NA > > $description > [1] "transcription factor activity" > [2] "nucleus" > [3] "transcription" > [4] "regulation of transcription, DNA-dependent" > [5] "apoptosis" > [6] "negative regulation of cell cycle" > [7] NA > > $evidence > [1] "IEA" "IEA" "IEA" "IEA" "IEA" "IEA" NA > > $martID > [1] "ENSRNOG00000010756" "ENSRNOG00000010756" "ENSRNOG00000010756" > [4] "ENSRNOG00000010756" "ENSRNOG00000010756" "ENSRNOG00000010756" > [7] "ENSRNOG00000010756" > > > > > > Dipl.-Ing. Johannes Rainer wrote: > >> hi, >> >> i wanted to build an annotation package for the Affymetrix rat2302 >> chip. because i have problems to access ftp servers through the >> http_proxy i am behind (it works perfectly with http, but not >> through the ftp protocol) i downloaded the LocusLink and UniGene >> database files and created my UG and LL objects with the option >> "fromWeb=FALSE". i supposed that it would work, but i got an error >> "could not open connection to >> ftp://ftp.ncbi.nih.gov/repository/UniGene/Rn.info". i supposed the >> function would not try to establish connections to the internet when >> i submit the attribute fromWeb=FALSE and define a local url >> beginning with file:// . maybe this is a bug, it may be better if >> one can submit also the url of a local info file to get the >> information about the built that was used... i wrote a wrapper >> function that overwrites the getUGBuilt() function to read a local >> info file, but it took me some time to understand why the call >> everytime failed >> >> another question: locuslink has been substituted by the Gene >> database... are there plans that AnnBuilder will annotate using the >> new database? >> >> thanks, jo >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > >