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Question: Error using makeGeneRegion/getBM/listFilters, argument 'what' contains an invalid value: type
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gravatar for T Joshi
8.0 years ago by
T Joshi90
T Joshi90 wrote:
Hi, I have been trying to work with an archived version of ensembl mart, i.e. ensembl_46. The code goes as follow: >library(biomaRt) >#listMarts(archive=TRUE) >mart=useMart("ensembl_mart_46", archive=TRUE) >## listDatasets(mart) >mart=useDataset("mmusculus_gene_ensembl",mart) Checking attributes ... ok Checking filters ... ok Warning messages: 1: In bmAttrFilt("attributes", mart) : biomaRt warning: looks like we're connecting to an older version of BioMart suite. Some biomaRt functions might not work. 2: In bmAttrFilt("filters", mart) : biomaRt warning: looks like we're connecting to an older version of BioMart suite. Some biomaRt functions might not work. > plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end = 30550000, strand = "+", biomart = mart) I have modified the GeneRegion method such that it can work with older, hardcoded attribute names. It started to give error once again due to "strand" not being one of the filters supported by old ensembl build. Therefore, I tried a simpler way to collect genomic features from biomart : > getBM(c("gene_stable_id","transcript_stable_id", "exon_stable_id","exon_chrom_start","exon_chrom_end", "rank", "transcript_chrom_strand","struct_biotype"), filters=c("chromosome_name","start","end"),values=list(17,30450000,304 55000),mart) Error in listFilters(mart, what = "type") : The function argument 'what' contains an invalid value: type Valid are: name, description, options, fullDescription I also tried out with listFilters function : listFilters("chromosome_name",mart=mart), which results in the same error. What is going on here, and how can I rectify it ? Here is my session info: R version 2.9.1 (2009-06-26) i386-apple-darwin8.11.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] GenomeGraphs_1.0.1 biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.94-1 XML_2.6-0 Thanks, Tejal [[alternative HTML version deleted]]
ADD COMMENTlink modified 8.0 years ago by steffen@stat.Berkeley.EDU600 • written 8.0 years ago by T Joshi90
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gravatar for steffen@stat.Berkeley.EDU
8.0 years ago by
Hi Tejal, Ensembl 46 is to old and there have been some major changes since for biomaRt to work with it. Would a more recent ensembl archive work for you? For example Ensembl 54 is NCBI36 and might be what you were looking for unless you have another reason to specifically want Ensembl 46? You can access Ensembl 54 like this: > 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) > ens54 = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl" ,host="may2009.archive.ensembl.org/biomart/martservice") Checking attributes and filters ... ok Cheers, Steffen > Hi, > I have been trying to work with an archived version of ensembl mart, i.e. > ensembl_46. The code goes as follow: > >>library(biomaRt) >>#listMarts(archive=TRUE) >>mart=useMart("ensembl_mart_46", archive=TRUE) >>## listDatasets(mart) >>mart=useDataset("mmusculus_gene_ensembl",mart) > Checking attributes ... ok > Checking filters ... ok > Warning messages: > 1: In bmAttrFilt("attributes", mart) : > biomaRt warning: looks like we're connecting to an older version of > BioMart suite. Some biomaRt functions might not work. > 2: In bmAttrFilt("filters", mart) : > biomaRt warning: looks like we're connecting to an older version of > BioMart suite. Some biomaRt functions might not work. > >> plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end >> = > 30550000, strand = "+", biomart = mart) > > > I have modified the GeneRegion method such that it can work with older, > hardcoded attribute names. It started to give error once again due to > "strand" not being one of the filters supported by old ensembl build. > Therefore, I tried a simpler way to collect genomic features from biomart > : > > > getBM(c("gene_stable_id","transcript_stable_id", > > "exon_stable_id","exon_chrom_start","exon_chrom_end", > "rank", > "transcript_chrom_strand","struct_biotype"), > > filters=c("chromosome_name","start","end"),values=list(17,30450000,3 0455000),mart) > > Error in listFilters(mart, what = "type") : > The function argument 'what' contains an invalid value: type > Valid are: name, description, options, fullDescription > > I also tried out with listFilters function : > listFilters("chromosome_name",mart=mart), which results in the same error. > > What is going on here, and how can I rectify it ? > > Here is my session info: > > R version 2.9.1 (2009-06-26) > i386-apple-darwin8.11.1 > > locale: > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] GenomeGraphs_1.0.1 biomaRt_2.0.0 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-1 XML_2.6-0 > > > Thanks, > Tejal > > [[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 >
ADD COMMENTlink written 8.0 years ago by steffen@stat.Berkeley.EDU600
Hi Steffen, You are right, this version is too old, but I need to use the older version. Any suggestions ? -Tejal On Wed, Nov 11, 2009 at 5:49 PM, <steffen@stat.berkeley.edu> wrote: > Hi Tejal, > > Ensembl 46 is to old and there have been some major changes since for > biomaRt to work with it. Would a more recent ensembl archive work for > you? > For example Ensembl 54 is NCBI36 and might be what you were looking for > unless you have another reason to specifically want Ensembl 46? > You can access Ensembl 54 like this: > > > 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) > > ens54 = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl" > ,host="may2009.archive.ensembl.org/biomart/martservice") > Checking attributes and filters ... ok > > > > Cheers, > Steffen > > > > > Hi, > > I have been trying to work with an archived version of ensembl mart, i.e. > > ensembl_46. The code goes as follow: > > > >>library(biomaRt) > >>#listMarts(archive=TRUE) > >>mart=useMart("ensembl_mart_46", archive=TRUE) > >>## listDatasets(mart) > >>mart=useDataset("mmusculus_gene_ensembl",mart) > > Checking attributes ... ok > > Checking filters ... ok > > Warning messages: > > 1: In bmAttrFilt("attributes", mart) : > > biomaRt warning: looks like we're connecting to an older version of > > BioMart suite. Some biomaRt functions might not work. > > 2: In bmAttrFilt("filters", mart) : > > biomaRt warning: looks like we're connecting to an older version of > > BioMart suite. Some biomaRt functions might not work. > > > >> plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, end > >> = > > 30550000, strand = "+", biomart = mart) > > > > > > I have modified the GeneRegion method such that it can work with older, > > hardcoded attribute names. It started to give error once again due to > > "strand" not being one of the filters supported by old ensembl build. > > Therefore, I tried a simpler way to collect genomic features from biomart > > : > > > > > getBM(c("gene_stable_id","transcript_stable_id", > > > > "exon_stable_id","exon_chrom_start","exon_chrom_end", > > "rank", > > "transcript_chrom_strand","struct_biotype"), > > > > > filters=c("chromosome_name","start","end"),values=list(17,30450000,3 0455000),mart) > > > > Error in listFilters(mart, what = "type") : > > The function argument 'what' contains an invalid value: type > > Valid are: name, description, options, fullDescription > > > > I also tried out with listFilters function : > > listFilters("chromosome_name",mart=mart), which results in the same > error. > > > > What is going on here, and how can I rectify it ? > > > > Here is my session info: > > > > R version 2.9.1 (2009-06-26) > > i386-apple-darwin8.11.1 > > > > locale: > > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > base > > > > other attached packages: > > [1] GenomeGraphs_1.0.1 biomaRt_2.0.0 > > > > loaded via a namespace (and not attached): > > [1] RCurl_0.94-1 XML_2.6-0 > > > > > > Thanks, > > Tejal > > > > [[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 REPLYlink written 8.0 years ago by T Joshi90
Hi Tejal, You'll need to do your query using the web interface at: http://aug2007.archive.ensembl.org/biomart/martview/ export as a tab delimited file and import that in R. Cheers, Steffen > Hi Steffen, > You are right, this version is too old, but I need to use the older > version. > Any suggestions ? > > -Tejal > > On Wed, Nov 11, 2009 at 5:49 PM, <steffen at="" stat.berkeley.edu=""> wrote: > >> Hi Tejal, >> >> Ensembl 46 is to old and there have been some major changes since for >> biomaRt to work with it. Would a more recent ensembl archive work for >> you? >> For example Ensembl 54 is NCBI36 and might be what you were looking for >> unless you have another reason to specifically want Ensembl 46? >> You can access Ensembl 54 like this: >> >> > 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) >> > ens54 = useMart("ENSEMBL_MART_ENSEMBL", >> dataset="hsapiens_gene_ensembl" >> ,host="may2009.archive.ensembl.org/biomart/martservice") >> Checking attributes and filters ... ok >> >> >> >> Cheers, >> Steffen >> >> >> >> > Hi, >> > I have been trying to work with an archived version of ensembl mart, >> i.e. >> > ensembl_46. The code goes as follow: >> > >> >>library(biomaRt) >> >>#listMarts(archive=TRUE) >> >>mart=useMart("ensembl_mart_46", archive=TRUE) >> >>## listDatasets(mart) >> >>mart=useDataset("mmusculus_gene_ensembl",mart) >> > Checking attributes ... ok >> > Checking filters ... ok >> > Warning messages: >> > 1: In bmAttrFilt("attributes", mart) : >> > biomaRt warning: looks like we're connecting to an older version of >> > BioMart suite. Some biomaRt functions might not work. >> > 2: In bmAttrFilt("filters", mart) : >> > biomaRt warning: looks like we're connecting to an older version of >> > BioMart suite. Some biomaRt functions might not work. >> > >> >> plusStrand = new("GeneRegion", chromosome = "17", start = 30450000, >> end >> >> = >> > 30550000, strand = "+", biomart = mart) >> > >> > >> > I have modified the GeneRegion method such that it can work with >> older, >> > hardcoded attribute names. It started to give error once again due to >> > "strand" not being one of the filters supported by old ensembl build. >> > Therefore, I tried a simpler way to collect genomic features from >> biomart >> > : >> > >> > > getBM(c("gene_stable_id","transcript_stable_id", >> > >> > "exon_stable_id","exon_chrom_start","exon_chrom_end", >> > "rank", >> > "transcript_chrom_strand","struct_biotype"), >> > >> > >> filters=c("chromosome_name","start","end"),values=list(17,30450000, 30455000),mart) >> > >> > Error in listFilters(mart, what = "type") : >> > The function argument 'what' contains an invalid value: type >> > Valid are: name, description, options, fullDescription >> > >> > I also tried out with listFilters function : >> > listFilters("chromosome_name",mart=mart), which results in the same >> error. >> > >> > What is going on here, and how can I rectify it ? >> > >> > Here is my session info: >> > >> > R version 2.9.1 (2009-06-26) >> > i386-apple-darwin8.11.1 >> > >> > locale: >> > en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> > >> > attached base packages: >> > [1] grid stats graphics grDevices utils datasets >> methods >> > base >> > >> > other attached packages: >> > [1] GenomeGraphs_1.0.1 biomaRt_2.0.0 >> > >> > loaded via a namespace (and not attached): >> > [1] RCurl_0.94-1 XML_2.6-0 >> > >> > >> > Thanks, >> > Tejal >> > >> > [[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 >> > >> >> >
ADD REPLYlink written 8.0 years ago by steffen@stat.Berkeley.EDU600
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