Job offer at EMBL Heidelberg
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@delhommeemblde-3232
Last seen 10.2 years ago
Hello, Might be interesting for some of you: Bioinformatician / Data Analyst Grade: 5 or 6, depending on experience EMBL site: EMBL Heidelberg Commencing date: As sooon as possible, after closing date Job description: EMBL is seeking for a Bioinformatician / Data Analyst in its efforts to build an expanded analysis-infrastructure for next- generation sequencing data. The successful candidate will primarily be involved in processing large-scale DNA sequencing data and in building analysis pipelines for such data, as a service for the EMBL research community. The person may also participate in the scientific development of new approaches for large-scale data analysis. The successful candidate will be associated with the Genomics Core Facility (Vladimir Benes) and with Jan Korbel?s EMBL Research Group pioneering new applications and analysis approaches for next- generation sequencing. The work will be carried out in an international and highly collaborative environment at the cutting edge of science, with a primary focus on service and the possibility to contribute to a range of research projects at EMBL. More details there: http://www- db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/09011.html Cheers, N.
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@arteaga-salas-jose-m-2497
Last seen 10.2 years ago
Dear List, I am running an experiment with some HG-U133A arrays. I identified some dodgy probes, and I have created an alternative CDF file without these probes. Now, I want to summarize my .CEL files with either rma() or just.rma() to analyze the impact of my dodgy probes in gene expression. I am trying to run these commands, and then obtaining this error: > data=ReadAffy(cdfname="MyAlternativeCdf.CDF"); > rma.alternative=rma(data,cdfname=" MyAlternativeCdf.CDF "); Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain MyAlternativeCdf.CDF Library - package MyAlternativeCdf.cdf not installed Bioconductor - MyAlternativeCdf.cdf not available My guess so far is that I am getting this error because of the C implementation of RMA, that I don't seem to have available in any folder of my "affy" package instalation. Is there anyway that I can get around this problem? Thank you for your kind replies. Jose Manuel Arteaga PhD Student in Statistics University of Essex, U.K.
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A CDF (chip definition/description file) is an Affymetrix CDF file (one file/no directory). In Bioconductor there are CDF packages also known as/that contains CDF environments. CDF packages can be created from CDF files. You need a CDF *package* - a CDF *file* will not work. So, argument 'cdfname' takes a package name. You are not the first one making this mistake. See also the aroma.affymetrix package which works with CDF files (including custom ones) directly. It can reproduce the results of both affy and affyPLM near perfectly. http://www.braju.com/R/aroma.affymetrix/ /Henrik On Fri, Jan 23, 2009 at 5:32 AM, Arteaga Salas, Jose M <jmarte at="" essex.ac.uk=""> wrote: > > Dear List, > > I am running an experiment with some HG-U133A arrays. > I identified some dodgy probes, and I have created an alternative CDF > file without these probes. > > Now, I want to summarize my .CEL files with either rma() or just.rma() > to analyze the impact of my dodgy probes in gene expression. > > > I am trying to run these commands, and then obtaining this error: > >> data=ReadAffy(cdfname="MyAlternativeCdf.CDF"); >> rma.alternative=rma(data,cdfname=" MyAlternativeCdf.CDF "); > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MyAlternativeCdf.CDF > Library - package MyAlternativeCdf.cdf not installed > Bioconductor - MyAlternativeCdf.cdf not available > > > My guess so far is that I am getting this error because of the C > implementation of RMA, that I don't seem to have available in any folder > of my "affy" package instalation. > > > Is there anyway that I can get around this problem? > > Thank you for your kind replies. > > > > Jose Manuel Arteaga > PhD Student in Statistics > University of Essex, U.K. > > _______________________________________________ > 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 >
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On Fri, Jan 23, 2009 at 8:32 AM, Arteaga Salas, Jose M <jmarte@essex.ac.uk>wrote: > > Dear List, > > I am running an experiment with some HG-U133A arrays. > I identified some dodgy probes, and I have created an alternative CDF > file without these probes. > > Now, I want to summarize my .CEL files with either rma() or just.rma() > to analyze the impact of my dodgy probes in gene expression. > > > I am trying to run these commands, and then obtaining this error: > > > data=ReadAffy(cdfname="MyAlternativeCdf.CDF"); > > rma.alternative=rma(data,cdfname=" MyAlternativeCdf.CDF "); > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MyAlternativeCdf.CDF > Library - package MyAlternativeCdf.cdf not installed > Bioconductor - MyAlternativeCdf.cdf not available > > > My guess so far is that I am getting this error because of the C > implementation of RMA, that I don't seem to have available in any folder > of my "affy" package instalation. > > > Is there anyway that I can get around this problem? > Actually, the problem is that you need to build a cdf environment. The cdf file is not directly useful for bioconductor. The package makecdfenv will do this for you. Just work through the vignette. Hope that helps. Sean [[alternative HTML version deleted]]
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Sean Davis wrote: > On Fri, Jan 23, 2009 at 8:32 AM, Arteaga Salas, Jose M > <jmarte at="" essex.ac.uk="">wrote: > >> Dear List, >> >> I am running an experiment with some HG-U133A arrays. >> I identified some dodgy probes, and I have created an alternative CDF >> file without these probes. >> >> Now, I want to summarize my .CEL files with either rma() or just.rma() >> to analyze the impact of my dodgy probes in gene expression. >> >> >> I am trying to run these commands, and then obtaining this error: >> >>> data=ReadAffy(cdfname="MyAlternativeCdf.CDF"); >>> rma.alternative=rma(data,cdfname=" MyAlternativeCdf.CDF "); >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain MyAlternativeCdf.CDF >> Library - package MyAlternativeCdf.cdf not installed >> Bioconductor - MyAlternativeCdf.cdf not available >> >> >> My guess so far is that I am getting this error because of the C >> implementation of RMA, that I don't seem to have available in any folder >> of my "affy" package instalation. >> >> >> Is there anyway that I can get around this problem? >> > > Actually, the problem is that you need to build a cdf environment. The cdf > file is not directly useful for bioconductor. The package makecdfenv will > do this for you. Just work through the vignette. You can also check the package altcdfenvs if you consider working on alternative CDF environmnents without wanting to handle CDF files. L. > Hope that helps. > > Sean > > [[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
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Hi All I am just learning to use biomaRt from R and could do with a little help please. I have worked my way through the user guide and "How to build a biomaRt" query and that has all worked fine. But now I am trying to build my own queries and have a couple of questions. Question 1 =========== I am using the Ensembl database. Looking at the www.ensembl.org website it looks like you do not have to specify a filter. Do you have to specify a filter using biomaRt/R? If not how is it done? Question 2 ============== While trying things I get the following error message, presumably caused by the attribute not being in that table. V1 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed Error in getBM(attnames, filters = filtnames, values = transcripts, mart = mart) : Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report. > How can I avoid this error other than by trial and error? Is there a bit more documentation somewhere that I have not found that describes the data structure/format in more detail? i.e. how to select the attributes that are not on "multiple attribute pages"? At the moment I am just building my queries by trying something and seeing if it works which does not seem right. I think there must be some more information that will make it a bit easier. Also I cannot find anything that describes the groups/categories/types and what they mean or do. Thank you for any help. Regards John ---
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Hi, > Question 1 > =========== > > I am using the Ensembl database. Looking at the www.ensembl.org > website > it looks like you do not have to specify a filter. Do you have to > specify a filter using biomaRt/R? If not how is it done? I'm not sure I get what you're getting at, and probably others will jump in to answer your question with ease (I'm also getting more acquainted w/ biomaRt), but could you give an example of a query you're trying to do that wouldn't use a filter? Perhaps one I can think of off hand would be to get all the gene id's for your organism. Intuitively you might think that there are no filters you can use in this case, but you do: you would use the chromosomes you want to get the info for (in this case, it would be all of them). So, you would just do something like: annos <- getBM(..., attributes='ensembl_gene_id', filters='chromosome_name', values=CHROMOSOMES) That's a butchered-for-brevity piece of code. There is an example in the recent Toedling and Huber chip-chip tutorial from plos compbio where they call getBM as many times as there are chromosomes and filter/collate afterwards. Anyway ... an example of the query you have in mind might help. > Question 2 > ============== > > While trying things I get the following error message, presumably > caused > by the attribute not being in that table. > > > V1 > 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed > Error in getBM(attnames, filters = filtnames, values = transcripts, > mart > = mart) : > Number of columns in the query result doesn't equal number of > attributes in query. This is probably an internal error, please > report. I was fighting with a similar error recently, I was using gene symbols/ names to look up annotation info for them. It turned out that some of my names had an apostrophe in the ('), and another gene name somehow had a "" tacked on to it. I received a gene list from an experimentalist and just didn't think to scrub it, so it took a while to figure out that that was the problem. Perhaps you have some illegal characters in your transcript names, too. HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos
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Hi Steve Thanks for the answers. I will go back and try again and perhaps make some progress. On your second point I will check for illegal characters; but the transcript names were returned from Biomart/Ensembl so they should be OK. Regards John Seers --- mailto:John.Seers at bbsrc.ac.uk John Seers Bioinformatics & Statistics Institute of Food Research Norwich Research Park Colney Norwich NR4 7UA Location: IFR1 N102 PC Machine ID: N198 tel +44 (0)1603 251497 fax +44 (0)1603 507723 e-mail john.seers at bbsrc.ac.uk e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ Web sites: www.ifr.ac.uk www.foodandhealthnetwork.com -----Original Message----- From: Steve Lianoglou [mailto:mailinglist.honeypot@gmail.com] Sent: 23 January 2009 16:46 To: john seers (IFR) Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Help using biomaRt Hi, > Question 1 > =========== > > I am using the Ensembl database. Looking at the www.ensembl.org > website > it looks like you do not have to specify a filter. Do you have to > specify a filter using biomaRt/R? If not how is it done? I'm not sure I get what you're getting at, and probably others will jump in to answer your question with ease (I'm also getting more acquainted w/ biomaRt), but could you give an example of a query you're trying to do that wouldn't use a filter? Perhaps one I can think of off hand would be to get all the gene id's for your organism. Intuitively you might think that there are no filters you can use in this case, but you do: you would use the chromosomes you want to get the info for (in this case, it would be all of them). So, you would just do something like: annos <- getBM(..., attributes='ensembl_gene_id', filters='chromosome_name', values=CHROMOSOMES) That's a butchered-for-brevity piece of code. There is an example in the recent Toedling and Huber chip-chip tutorial from plos compbio where they call getBM as many times as there are chromosomes and filter/collate afterwards. Anyway ... an example of the query you have in mind might help. > Question 2 > ============== > > While trying things I get the following error message, presumably > caused > by the attribute not being in that table. > > > V1 > 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed > Error in getBM(attnames, filters = filtnames, values = transcripts, > mart > = mart) : > Number of columns in the query result doesn't equal number of > attributes in query. This is probably an internal error, please > report. I was fighting with a similar error recently, I was using gene symbols/ names to look up annotation info for them. It turned out that some of my names had an apostrophe in the ('), and another gene name somehow had a "" tacked on to it. I received a gene list from an experimentalist and just didn't think to scrub it, so it took a while to figure out that that was the problem. Perhaps you have some illegal characters in your transcript names, too. HTH, -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Medical College of Cornell University http://cbio.mskcc.org/~lianos
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Hi John, > Question 1 > =========== > > I am using the Ensembl database. Looking at the www.ensembl.org website > it looks like you do not have to specify a filter. Do you have to > specify a filter using biomaRt/R? If not how is it done? > No you don't have to specify a filter and associated values. You can do for example: mart = useMart("ensembl",dataset="hsapiens_gene_ensembl") ensid = getBM(attributes="ensembl_gene_id", mart=mart) This will return all ensembl gene identifiers. > Question 2 > ============== > > While trying things I get the following error message, presumably caused > by the attribute not being in that table. > > > V1 > 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed > Error in getBM(attnames, filters = filtnames, values = transcripts, mart > = mart) : > Number of columns in the query result doesn't equal number of > attributes in query. This is probably an internal error, please report. >> > > How can I avoid this error other than by trial and error? Is there a bit > more documentation somewhere that I have not found that describes the > data structure/format in more detail? i.e. how to select the attributes > that are not on "multiple attribute pages"? At the moment I am just > building my queries by trying something and seeing if it works which > does not seem right. I think there must be some more information that > will make it a bit easier. > > Also I cannot find anything that describes the groups/categories/types > and what they mean or do. > You can see to which attribute page an attribute belongs using the function listAttributes(mart, showGroups = TRUE) note that if you're using the developmental version of biomaRt you can get this information with: listAttributes(mart, what=c("name","page")) hope this helps. Best, Steffen
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Hi Steffen Thanks for the suggested ways forward. I will try again ... Regards John Seers --- mailto:John.Seers at bbsrc.ac.uk John Seers Bioinformatics & Statistics Institute of Food Research Norwich Research Park Colney Norwich NR4 7UA Location: IFR1 N102 PC Machine ID: N198 tel +44 (0)1603 251497 fax +44 (0)1603 507723 e-mail john.seers at bbsrc.ac.uk e-disclaimer at http://www.ifr.ac.uk/edisclaimer/ Web sites: www.ifr.ac.uk www.foodandhealthnetwork.com -----Original Message----- From: steffen@stat.Berkeley.EDU [mailto:steffen@stat.Berkeley.EDU] Sent: 25 January 2009 23:20 To: john seers (IFR) Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Help using biomaRt Hi John, > Question 1 > =========== > > I am using the Ensembl database. Looking at the www.ensembl.org website > it looks like you do not have to specify a filter. Do you have to > specify a filter using biomaRt/R? If not how is it done? > No you don't have to specify a filter and associated values. You can do for example: mart = useMart("ensembl",dataset="hsapiens_gene_ensembl") ensid = getBM(attributes="ensembl_gene_id", mart=mart) This will return all ensembl gene identifiers. > Question 2 > ============== > > While trying things I get the following error message, presumably caused > by the attribute not being in that table. > > > V1 > 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed > Error in getBM(attnames, filters = filtnames, values = transcripts, mart > = mart) : > Number of columns in the query result doesn't equal number of > attributes in query. This is probably an internal error, please report. >> > > How can I avoid this error other than by trial and error? Is there a bit > more documentation somewhere that I have not found that describes the > data structure/format in more detail? i.e. how to select the attributes > that are not on "multiple attribute pages"? At the moment I am just > building my queries by trying something and seeing if it works which > does not seem right. I think there must be some more information that > will make it a bit easier. > > Also I cannot find anything that describes the groups/categories/types > and what they mean or do. > You can see to which attribute page an attribute belongs using the function listAttributes(mart, showGroups = TRUE) note that if you're using the developmental version of biomaRt you can get this information with: listAttributes(mart, what=c("name","page")) hope this helps. Best, Steffen
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Hi All And thanks to all those that have helped. My biomart query is now working fine and I can get what I want with two queries, the second query using a different filter. But I still feel I built my query by trial and error rather than in an intelligent way. I have used Steffen's suggestion to use listAttributes to understand the attributes grouping/category but that does not seem to help me much. So the question is how could I have avoided blundering into this error: #1 Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed Here is an example of me going wrong: library(biomaRt) # Connect to the mart mart<-useMart("ensembl") # Update the mart connection to use this dataset mart<-useDataset("mmusculus_gene_ensembl", mart=mart) # Just select a couple of affyids for testing affyids<-c("5325539", "5555964") # Build vector of filters filtnames<-"affy_moex_1_0_st_v1" # Build vector of attributes attnames<-c("affy_moex_1_0_st_v1", "ensembl_gene_id", "canonical_transcript_stable_id") # Submit biomart query results1<-getBM(attnames, filters=filtnames, values=affyids, mart=mart) # Great, that works. # But I would like to get some exon information as well # Thinks - how? # Check the attributes categories/groups: #listAttributes(mart, showGroups = TRUE)[c(9, 17, 28, 30, 678, 682),] # name description group category #9 affy_moex_1_0_st_v1 Affy MoEx EXTERNAL: Features #17 canonical_transcript_stable_id Canonical transcript stable ID(s) GENE: Features #28 ensembl_gene_id Ensembl Gene ID GENE: Features #30 ensembl_transcript_id Ensembl Transcript ID GENE: Features #678 ensembl_exon_id Ensembl Exon ID EXON: Structures #682 rank Exon Rank in Transcript EXON: Structures # Oh dear. Looks like exon information is in EXON: Structures # I guess that will not work ... # But I do not know what I am doing, so try adding exon rank anyway. # Build vector of attributes attnames<-c("affy_moex_1_0_st_v1", "ensembl_gene_id", "canonical_transcript_stable_id", "rank") # Submit biomart query results2<-getBM(attnames, filters=filtnames, values=affyids, mart=mart) # Great, that works! So add the exon id attribute. # Build vector of attributes attnames<-c("affy_moex_1_0_st_v1", "ensembl_gene_id", "canonical_transcript_stable_id", "rank", "ensembl_exon_id") # Submit biomart query results3<-getBM(attnames, filters=filtnames, values=affyids, mart=mart) # Fails .... # # V1 #1 Query ERROR: caught BioMart::Exception::Usage: Attributes from multiple attribute pages are not allowed #Error in getBM(attnames, filters = filtnames, values = affyids, mart = mart) : # Number of columns in the query result doesn't equal number of attributes in query. This is probably an internal error, please report. # Disconnect from biomart martDisconnect(mart) ###################################################################### ## ############################################## ###################################################################### ## ######################################### > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United Kingdom.1252;LC_MONETARY=English_United Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_1.16.0 RWinEdt_1.8-0 loaded via a namespace (and not attached): [1] RCurl_0.94-0 XML_1.99-0 > ---
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Hi John, You can do: > library(biomaRt) Loading required package: RCurl > mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") Checking attributes and filters ... ok > att=listAttributes(mart, category="Features") > att[1:10,] name description 1 affy_hc_g110 Affy HC G110 2 affy_hg_focus Affy HG FOCUS 3 affy_hg_u133_plus_2 Affy HG U133-PLUS-2 4 affy_hg_u133a Affy HG U133A 5 affy_hg_u133a_2 Affy HG U133A_2 6 affy_hg_u133b Affy HG U133B 7 affy_hg_u95a Affy HG U95A 8 affy_hg_u95av2 Affy HG U95AV2 9 affy_hg_u95b Affy HG U95B 10 affy_hg_u95c Affy HG U95C To get an overview of the possible categories you can do > attributeSummary(mart) category group 1 Features EXTERNAL: 2 Features EXPRESSION: 3 Features GENE: 4 Features PROTEIN DOMAINS: 5 Homologs AEDES ORTHOLOGS: This lists for example all attributes that are in the Features category(page). This is a bit easier to interpret on the web browser based BioMart interface (try one on http://www.biomart.org). There, attributes are grouped in different web pages so there is no possibility for users to select attributes from different pages as only attributes from one page are visible. The dev version of biomaRt now checks at the R side if all attributes are from the same page and will provide a warning before sending out the query to the BioMart web service. Note also that in the dev version we use the term page instead of category in order to be more compatible with the BioMart nomenclature. Cheers, Steffen > > Hi All > > And thanks to all those that have helped. > > My biomart query is now working fine and I can get what I want with two > queries, the second query using a different filter. > > But I still feel I built my query by trial and error rather than in an > intelligent way. I have used Steffen's suggestion to use listAttributes > to understand the attributes grouping/category but that does not seem to > help me much. > > > So the question is how could I have avoided blundering into this error: > > #1 Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed > > > Here is an example of me going wrong: > > library(biomaRt) > > > # Connect to the mart > mart<-useMart("ensembl") > # Update the mart connection to use this dataset > mart<-useDataset("mmusculus_gene_ensembl", mart=mart) > > # Just select a couple of affyids for testing > affyids<-c("5325539", "5555964") > > > # Build vector of filters > filtnames<-"affy_moex_1_0_st_v1" > # Build vector of attributes > attnames<-c("affy_moex_1_0_st_v1", "ensembl_gene_id", > "canonical_transcript_stable_id") > # Submit biomart query > results1<-getBM(attnames, filters=filtnames, values=affyids, mart=mart) > > # Great, that works. > # But I would like to get some exon information as well > # Thinks - how? > # Check the attributes categories/groups: > #listAttributes(mart, showGroups = TRUE)[c(9, 17, 28, 30, 678, 682),] > # name description > group category > #9 affy_moex_1_0_st_v1 Affy MoEx > EXTERNAL: Features > #17 canonical_transcript_stable_id Canonical transcript stable ID(s) > GENE: Features > #28 ensembl_gene_id Ensembl Gene ID > GENE: Features > #30 ensembl_transcript_id Ensembl Transcript ID > GENE: Features > #678 ensembl_exon_id Ensembl Exon ID > EXON: Structures > #682 rank Exon Rank in Transcript > EXON: Structures > > # Oh dear. Looks like exon information is in EXON: Structures > # I guess that will not work ... > # But I do not know what I am doing, so try adding exon rank anyway. > > # Build vector of attributes > attnames<-c("affy_moex_1_0_st_v1", "ensembl_gene_id", > "canonical_transcript_stable_id", "rank") > # Submit biomart query > results2<-getBM(attnames, filters=filtnames, values=affyids, mart=mart) > > # Great, that works! So add the exon id attribute. > > # Build vector of attributes > attnames<-c("affy_moex_1_0_st_v1", "ensembl_gene_id", > "canonical_transcript_stable_id", "rank", "ensembl_exon_id") > # Submit biomart query > results3<-getBM(attnames, filters=filtnames, values=affyids, mart=mart) > > # Fails .... > # > # > V1 > #1 Query ERROR: caught BioMart::Exception::Usage: Attributes from > multiple attribute pages are not allowed > #Error in getBM(attnames, filters = filtnames, values = affyids, mart = > mart) : > # Number of columns in the query result doesn't equal number of > attributes in query. This is probably an internal error, please report. > > > > # Disconnect from biomart > martDisconnect(mart) > > #################################################################### #### > ############################################## > > > > > > #################################################################### #### > ######################################### > >> sessionInfo() > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > > other attached packages: > [1] biomaRt_1.16.0 RWinEdt_1.8-0 > > loaded via a namespace (and not attached): > [1] RCurl_0.94-0 XML_1.99-0 >> > > > --- > >
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Hi Steffen Thank you very much for the reply. I am now pretty much sorted out for the queries I needed. Thanks for the help. I used the various commands successfully to list the categories and groups but what is a puzzle is this did not really help to understand which pages they belonged to or how to build the query. In my example I use "rank" and "ensembl_exon_id" which are both from "EXON: Structures" but they do not apparently work together, at least in this query. I guess I am missing something. Perhaps there are not hard edges to these pages. >This is a bit easier to interpret on the web browser based BioMart >interface (try one on http://www.biomart.org). Yes, exactly what I did but using www.ensembl.org. Once I had been round the houses a few times that was very helpful. >The dev version of biomaRt now checks at the R side if all attributes are >from the same page and will provide a warning before sending out the query >to the BioMart web service. Note also that in the dev version we use the >term page instead of category in order to be more compatible with the >BioMart nomenclature. These sound very good enhancements. I suggest that there might still be a need for some help in understanding what will work with what, so trial and error is not the only approach. The examples in the pdf are very good and very helpful to get started. Perhaps more working examples would be an idea - perhaps a repository of biomart queries? Regards John
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