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Question: BioMart and Ensembl questions
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gravatar for jiayu wen
8.2 years ago by
jiayu wen10
jiayu wen10 wrote:
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]]
ADD COMMENTlink modified 8.2 years ago by Paul Leo970 • written 8.2 years ago by jiayu wen10
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gravatar for Paul Leo
8.2 years ago by
Paul Leo970
Paul Leo970 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@gmail.com> To: bioconductor@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@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]]
ADD COMMENTlink written 8.2 years ago by Paul Leo970
Hi Paul, You can get access to archived ensembl marts by going to the following link: 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@gmail.com> > To: bioconductor@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@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@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. [[alternative HTML version deleted]]
ADD REPLYlink written 8.2 years ago by Rhoda Kinsella660
Sorry, I should have put the release 51 URI into the biomaRt package instead of release 54 :). Here it is: > library(biomaRt) > listMarts(host="nov2008.archive.ensembl.org/biomart/martservice") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl 51 2 ENSEMBL_MART_SNP Variation 51 3 ENSEMBL_MART_VEGA Vega 32 > etc.... Rhoda On 21 Sep 2009, at 14:40, Rhoda Kinsella wrote: > Hi Paul, > You can get access to archived ensembl marts by going to the following > link: > > 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. > > > [[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.
ADD REPLYlink written 8.2 years ago by Rhoda Kinsella660
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=TR UE) > > 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=TR UE) > 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.
ADD REPLYlink written 8.2 years ago by Paul Leo970
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.
ADD REPLYlink written 8.2 years ago by Rhoda Kinsella660
Rhoda Kinsella wrote: > 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? Yes. In your version of biomaRt, the URI is constructed like this: registry = getURL(paste(host, "?type=registry&requestid=biomaRt", sep = "")) whereas in the current and devel versions, the URI is constructed like this: registry = bmRequest(paste("http://", host, ":", port, path, "?type=registry&requestid=biomaRt", sep = "")) And http://nov2008.archive.ensembl.org/biomart/martservice:80/biomart/mart service?type=registry&requestid=biomaRt will result in a 404 error from the Biomart server. If you modify the host to "nov2008.archive.ensembl.org", you still get a busted URI. The only way I could get it to work is by running through the debugger and substituting something reasonable in after the registry object is created. Best, Jim > 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. > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLYlink written 8.2 years ago by James W. MacDonald45k
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/martservic e",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_posit ion","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@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.
ADD REPLYlink written 8.2 years ago by Paul Leo970
Hi Paul, 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/martserv ice",archive=TRUE) > mart=useMart("ensembl_mart_51", dataset="hsapiens_gene_ensembl", > host="may2009.archive.ensembl.org",path="/biomart/martservice",archi ve=TRUE) > > works BUT queries then fail: > > ann<-getBM(attributes = > c( "ensembl_gene_id","external_gene_id","chromosome_name","start_pos ition","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 How do you expect a chromosome name of NA to retrieve anything? This won't work regardless of the mart. ## first try with 'regular' mart... > library(biomaRt) > att <- c("ensembl_gene_id", "external_gene_id", "chromosome_name","start_position", "end_position","strand","hgnc_symbol") > a.filter <- c("chromosome_name","start","end") > fil.vals <- list(NA, 67325000,67620000) > mart <- useMart("ensembl","hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > getBM(att, a.filter, fil.vals, mart) [1] ensembl_gene_id external_gene_id chromosome_name start_position [5] end_position strand hgnc_symbol <0 rows> (or 0-length row.names) ## can't retrieve with an NA chromosome. try chromosome 1 > fil.vals[[1]] <- 1 > getBM(att, a.filter, fil.vals, mart) ensembl_gene_id external_gene_id chromosome_name start_position end_position 1 ENSG00000152763 WDR78 1 67278574 67390570 2 ENSG00000198160 MIER1 1 67390640 67454302 3 ENSG00000116704 SLC35D1 1 67469679 67520080 4 ENSG00000203963 C1orf141 1 67557859 67594220 strand hgnc_symbol 1 -1 WDR78 2 1 MIER1 3 -1 SLC35D1 4 -1 C1orf141 ## now let's try an archive... mart <- useMart("ensembl_mart_51", dataset="hsapiens_gene_ensembl", + host="may2009.archive.ensembl.org",path="/biomart/martservice",archive =TRUE) Checking attributes ... ok Checking filters ... ok > > getBM(att, a.filter, fil.vals, mart) ensembl_gene_id external_gene_id chromosome_name start_position end_position 1 ENSG00000221076 AL389925.10 1 67505872 67505998 2 ENSG00000203963 C1orf141 1 67330447 67366808 3 ENSG00000210924 AL133320.8 1 67340919 67341049 4 ENSG00000162594 IL23R 1 67404757 67498236 5 ENSG00000210928 AL109843.25 1 67434415 67434511 6 ENSG00000210936 AL389925.10 1 67505870 67505998 7 ENSG00000081985 IL12RB2 1 67545635 67635171 8 ENSG00000217598 RP4-763G1.1 1 67516323 67517050 9 ENSG00000221733 AL109843.25 1 67477711 67477798 strand hgnc_symbol 1 -1 2 -1 C1orf141 3 -1 4 1 IL23R 5 1 6 -1 7 1 IL12RB2 8 1 9 -1 Best, Jim > > > 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. > > _______________________________________________ > 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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826
ADD REPLYlink written 8.2 years ago by James W. MacDonald45k
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.
ADD REPLYlink written 8.2 years ago by Rhoda Kinsella660
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 >
ADD REPLYlink written 8.2 years ago by steffen@stat.Berkeley.EDU600
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/martservic e",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@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 >
ADD REPLYlink written 8.2 years ago by Paul Leo970
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
ADD REPLYlink written 8.2 years ago by jiayu wen60
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