Hi Paul and others, Thanks for responding my questions. I will try these suggestions. Jean On Sep 22, 2009, at 2:41 AM, Paul Leo wrote: > > Just so this thread has a tidy conclusion: > > with the development and production version to get to NCBI36 use as > follows: > > Choose you archive version use > > http://www.ensembl.org/index.html (follow BioMart tab and then "View > in > archive site" and the bottom of the page). Click on the archive > version > and the URl in the browser will give you the host to use below: > > > library(biomaRt) > listMarts(host="may2009.archive.ensembl.org",path="/biomart/ > martservice",archive=FALSE) > ### NOTE use archive=FALSE (I had TRUE before which was incorrect) > ### that will give you the name of the "biomart" to use > ENSEMBL_MART_ENSEMBL in my case > > #### say you wanted human then use (again archive=FALSE is new if you > ### want higher than ensemble_mart_51 > > mart=useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", > host="may2009.archive.ensembl.org",path="/biomart/ > martservice",archive=FALSE) > > All else is then as usual. Though watch out for that "NA" > chromosome ;-) > > Cheers > Paul > > > > > > > > -----Original Message----- > From: Steffen at stat.Berkeley.EDU > To: Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> > Cc: Paul Leo <p.leo at="" uq.edu.au="">, bioconductor > <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] BioMart and Ensembl questions !!! > Date: Mon, 21 Sep 2009 10:56:02 -0700 (PDT) > > Hi Paul, Rhoda, > > Jim's earlier suggestion should fix this. You need to specify a > value for > the chromosome name you're interested in. > > fil.vals = list(1,67325000,67620000) > > Then your query should return results (if there are any genes in this > region). > > Cheers, > Steffen > >> Hi Paul, >> It looks like you are using an unstable version of biomaRt (R version >> 2.10.0 Under development (unstable) (2009-09-20 r49770)) >> so can you try this with the 2.9.0 version and see if that works? Let >> me know how you get on. >> Regards, >> Rhoda >> >> On 21 Sep 2009, at 15:23, Paul Leo wrote: >> >>> HI Rhoda, >>> Yes a different version is probably it . There is STILL something >>> wrong, based on your suggestions: >>> >>> library(biomaRt) >>> listMarts(host="may2009.archive.ensembl.org",path="/biomart/ >>> martservice",archive=TRUE) >>> mart=useMart("ensembl_mart_51", dataset="hsapiens_gene_ensembl", >>> host="may2009.archive.ensembl.org",path="/biomart/ >>> martservice",archive=TRUE) >>> >>> works BUT queries then fail: >>> >>> ann<-getBM(attributes = >>> c >>> ( "ensembl_gene_id >>> ","external_gene_id >>> ","chromosome_name >>> ","start_position >>> ","end_position","strand","hgnc_symbol","gene_biotype"), filters = >>> a.filter, values=fil.vals, mart = mart) >>>> ann >>> [1] ensembl_gene_id external_gene_id chromosome_name >>> start_position >>> [5] end_position strand hgnc_symbol >>> <0 rows> (or 0-length row.names) >>> >>> >>>> a.filter >>> [1] "chromosome_name" "start" "end" >>>> fil.vals >>> [[1]] >>> [1] NA >>> >>> [[2]] >>> [1] 67325000 >>> >>> [[3]] >>> [1] 67620000 >>> >>> >>> I will try again tomorrow... it's late at night in Australia.... >>> >>> >>> >>> -----Original Message----- >>> From: Rhoda Kinsella <rhoda at="" ebi.ac.uk=""> >>> To: Paul Leo <p.leo at="" uq.edu.au=""> >>> Cc: bioconductor <bioconductor at="" stat.math.ethz.ch=""> >>> Subject: Re: [BioC] BioMart and Ensembl questions !!! >>> Date: Mon, 21 Sep 2009 15:10:42 +0100 >>> >>> Hi Paul >>> I'm not really sure why you get this error... I am using the >>> following >>> version: >>> >>>> sessionInfo() >>> R version 2.8.0 (2008-10-20) >>> i386-apple-darwin8.11.1 >>> >>> locale: >>> en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] biomaRt_1.16.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_0.92-0 XML_1.98-1 >>> >>> Does anyone know why Paul is getting this error? >>> Regards, >>> Rhoda >>> >>> >>> On 21 Sep 2009, at 14:53, Paul Leo wrote: >>> >>>> HI Rhoda , >>>> Thanks that seems exactly like I want but .. but it does not work >>>> for >>>> me... >>>> >>>> library(biomaRt) >>>>> listMarts(host="nov2008.archive.ensembl.org/biomart/martservice") >>>> Entity 'nbsp' not defined >>>> Entity 'nbsp' not defined >>>> Entity 'nbsp' not defined >>>> Entity 'nbsp' not defined >>>> Entity 'nbsp' not defined >>>> Entity 'nbsp' not defined >>>> Entity 'copy' not defined >>>> Entity 'nbsp' not defined >>>> Entity 'nbsp' not defined >>>> Error in names(x) <- value : >>>> 'names' attribute [2] must be the same length as the vector [0] >>>>> >>>> >>>> >>>> >>>> >>>> http://www.ensembl.org/info/website/archives/ >>>> >>>> >>>> Once you are there, click on the release you would like to look at >>>> and >>>> then on the biomart button. This will give you the >>>> URI you need to use >>>> in the biomaRt package to get access to that archive. For example >>>> the release 51 archive biomart is >>>> available at: >>>> >>>> >>>> http://nov2008.archive.ensembl.org/biomart/martview/ >>>> >>>> >>>> If you then >>>> plug this into biomart you can get access to the information you >>>> require: >>>> >>>> >>>>> library(biomaRt) >>>>> listMarts(host="may2009.archive.ensembl.org/biomart/martservice") >>>> biomart version >>>> 1 ENSEMBL_MART_ENSEMBL Ensembl 54 >>>> 2 ENSEMBL_MART_SNP Ensembl Variation 54 >>>> 3 ENSEMBL_MART_VEGA Vega 35 >>>> 4 REACTOME Reactome(CSHL US) >>>> 5 wormbase_current WormBase (CSHL US) >>>> 6 pride PRIDE (EBI UK) >>>>> mart=useMart("ENSEMBL_MART_ENSEMBL", >>>> host="may2009.archive.ensembl.org/biomart/martservice") >>>> >>>> >>>> etc.... >>>> >>>> >>>> I hope that helps, >>>> Regards, >>>> Rhoda >>>> >>>> >>>> >>>> >>>> >>>> >>>> On 21 Sep 2009, at 14:25, Paul Leo wrote: >>>> >>>>> Wow that is fairly terrible , I was surprised this thread was not >>>>> followed... did I miss something? >>>>> >>>>> You can't access hg18 via BioMART only CRCh37!! >>>>> >>>>> 1)listMarts(archive=TRUE) # shows mart back to 43 are there >>>>> >>>>> I'll start tracking back >>>>> >>>>> >>>>> 2)mart<- >>>>> useMart("ensembl_mart_51",dataset="hsapiens_gene_ensembl",archive >>>>> ### WORKS FINE but is CRCh37 >>>>> >>>>> 3)mart<- >>>>> useMart >>>>> ("ensembl_mart_50",dataset="hsapiens_gene_ensembl",archive=TRUE) >>>>> >>>>> Error in value[[3L]](cond) : >>>>> Request to BioMart web service failed. Verify if you are still >>>>> connected to the internet. Alternatively the BioMart web >>>>> service is >>>>> temporarily down. >>>>> In addition: Warning message: >>>>> In file(file, "r") : unable to resolve >>>>> 'july2008.archive.ensembl.org' >>>>>> ##### THAT's JUST BAD ! >>>>> >>>>> 4)mart<- >>>>> useMart >>>>> ("ensembl_mart_49",dataset="hsapiens_gene_ensembl",archive=TRUE) >>>>> Checking attributes ... ok >>>>> Checking filters ... ok >>>>> Warning message: >>>>> In bmAttrFilt("filters", mart) : >>>>> biomaRt warning: looks like we're connecting to an older version >>>>> of >>>>> BioMart suite. Some biomaRt functions might not work. >>>>> >>>>> . ### works but that is NCBI36 but the attributes have old >>>>> descriptions >>>>> but may work for you (and me) >>>>> >>>>> >>>>> >>>>> I think 'july2008.archive.ensembl.org' SHOULD BE >>>>> 'jul2008.archive.ensembl.org' >>>>> (three letter month name) >>>>> >>>>> Anyway to fix that? >>>>> >>>>> Cheers >>>>> Paul >>>>> >>>>> NOTE also broken in production version 2.9.2 I think >>>>> >>>>>> sessionInfo() >>>>> R version 2.10.0 Under development (unstable) (2009-09-20 r49770) >>>>> x86_64-unknown-linux-gnu >>>>> >>>>> locale: >>>>> [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C >>>>> [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 >>>>> [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 >>>>> [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C >>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C >>>>> >>>>> attached base packages: >>>>> [1] stats graphics grDevices utils datasets methods >>>>> base >>>>> >>>>> other attached packages: >>>>> [1] biomaRt_2.1.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] RCurl_1.2-0 XML_2.6-0 >>>>> >>>>> -----Original Message----- >>>>> From: jiayu wen <jiayu.jwen at="" gmail.com=""> >>>>> To: bioconductor at stat.math.ethz.ch >>>>> Subject: [BioC] BioMart and Ensembl questions >>>>> Date: Tue, 1 Sep 2009 09:11:09 +0200 >>>>> >>>>> >>>>> Dear list, >>>>> >>>>> About over a year ago, I extracted 3'UTR sequences for about 7000 >>>>> genes using Biomart for my project. This is the command that I >>>>> used: >>>>> >>>>> (my gene_list is in gene symbol) >>>>>> my_mart = useMart("ensembl",dataset="hsapiens_gene_ensembl") >>>>>> seq_3utr = getSequence(id = unique(gene.symbol), >>>>> type="hgnc_symbol",seqType="3utr",mart = my_mart) >>>>>> seq_3utr = seq_3utr[seq_3utr[,"3utr"] != "Sequence unavailable",] >>>>>> here: extract longest 3'UTR for each unique gene symbol >>>>>> exportFASTA(seq_3utr, file=paste("s3utr.fa",sep="")) >>>>> >>>>> As my project goes, I now need 3'UTR genomic coordinates to get >>>>> phastcons conservation for some regions in 3'UTR. >>>>> To do that, I first convert hgnc_symbol back to ensembl_gene_id, >>>>> then >>>>> >>>>> get 3'UTR coordinates using getBM like this: >>>>> >>>>>> s3utr = >>>>>> read.DNAStringSet(paste("s3utr.fa",sep=""),format="fasta") >>>>>> gene_names = names(s3utr) >>>>>> hgnc2ensembl = >>>>>> getBM(attributes=c("hgnc_symbol","ensembl_gene_id"), >>>>> filters="hgnc_symbol", values=gene_names, mart=my_mart) >>>>>> s3utr_pos = getBM(attributes=c("ensembl_gene_id", >>>>> "chromosome_name","strand","3_utr_start", "3_utr_end"), >>>>> filters="ensembl_gene_id", values=as.character(hgnc2ensembl >>>>> $ensembl_gene_id), mart=my_mart) >>>>>> s3utr_pos = s3utr_pos[complete.cases(s3utr_pos),] >>>>> >>>>> By doing that, now I can only get about 5000 gene symbols with >>>>> 3'UTR >>>>> coordinates (converting from hgnc_symbol back to ensembl_gene_id >>>>> looses about 250 genes). I was thinking it might be version >>>>> difference? So I tried to use ensembl archive but it gives me >>>>> error >>>>> as >>>>> below: >>>>> >>>>>> my_mart = >>>>> useMart >>>>> ("ensembl_mart_50",dataset="hsapiens_gene_ensembl",archive=T) >>>>> Error in value[[3L]](cond) : >>>>> Request to BioMart web service failed. Verify if you are still >>>>> connected to the internet. Alternatively the BioMart web >>>>> service is >>>>> temporarily down. >>>>> In addition: Warning message: >>>>> In file(file, "r") : cannot open: HTTP status was '404 Not Found' >>>>> >>>>> Is there anyway that I can get 3'UTR coordinates for all my gene >>>>> list? >>>>> >>>>> Thanks for any help. >>>>> >>>>> Jean >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> [[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>> >>>> Rhoda Kinsella Ph.D. >>>> Ensembl Bioinformatician, >>>> European Bioinformatics Institute (EMBL-EBI), >>>> Wellcome Trust Genome Campus, >>>> Hinxton >>>> Cambridge CB10 1SD, >>>> UK. >>>> >>>> >>> >>> Rhoda Kinsella Ph.D. >>> Ensembl Bioinformatician, >>> European Bioinformatics Institute (EMBL-EBI), >>> Wellcome Trust Genome Campus, >>> Hinxton >>> Cambridge CB10 1SD, >>> UK. >>> >> >> Rhoda Kinsella Ph.D. >> Ensembl Bioinformatician, >> European Bioinformatics Institute (EMBL-EBI), >> Wellcome Trust Genome Campus, >> Hinxton >> Cambridge CB10 1SD, >> UK. >> >> _______________________________________________ >> 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