Hi Quin, It can deal with a long vector of identifiers e,g, 30000 ids should work in one query and should be fast. Cheers, Steffen Quin Wills wrote: > Thank you Steffen for the really quick reply. > > Out of interest, I tried using Sys.sleep() but I still get the same > problem. www.ensembl.org is also running quite slowly this side for > queries, and I wonder if that might be somehow related. > > Sorry if this is in the manual - I didn't spot it. How many queries in > a batch do you think one should avoid going over? I've a fairly long > list of identifiers. > > Quin > > > Steffen wrote: >> Hi Quin, >> >> How long is your list of identifiers? It is not recommended to run a >> query like this in loops as this causes the web service to go out of >> sync at some point during the loop. >> biomaRt is made to perform batch queries. >> I would recommend to do your query as follows: >> >> genes <- getGene(id=ID, type="refseq_dna", mart=ensembl) >> >> This will give you a dataframe with the info for all the genes. If >> needed you can then loop over the result. >> If you feel like you really need to loop you could add Sys.sleep(1) >> in the loop. >> >> Cheers, >> Steffen >> >> Quin Wills wrote: >>> Hello all >>> >>> I'm running the most up to date R and biomaRt. >>> >>> I get the following error: >>> >Error: ncol(result) == length(attributes) is not TRUE >>> >>> for the following loop: >>> # 'ID' is a character vector of refseq IDs >>> #'gene', for the purposes of the argument here, is a list storing >>> the output >>> >>> > ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl") >>> > for (i in 1:length(ID)) { >>> > gene[[i]] <- getGene(id=ID[i], type="refseq_dna", >>> mart=ensembl) >>> > } >>> >>> The problem is not dependent on the get function used or the id type >>> used. I didn't have this problem yesterday on the same script. The >>> error also occurs randomly, breaking the loop at any particular >>> point, sometimes allowing thousands of loops to run. >>> >>> Could this be a problem with the server I'm pulling the information >>> from? It just seems too random to be my coding - especially >>> considering I didn't have this problem yesterday. >>> >>> I've had this before, ages ago, and would like to get to the bottom >>> of it. And wisdom? Thanks. >>> >>> >>> * * >>> >>> * * >>> >>> * * >>> >>> *Quin Wills* >>> *DPhil candidate* >>> >>> * * >>> >>> *Department of Statistics* >>> >>> *University** of Oxford*** >>> >>> *1 South Parks Road* >>> *Oxford*** >>> >>> *OX1 3TG >>> United Kingdom* >>> >>> >>> >>> *01865 285 394* >>> >>> >>> [[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 >>> >>> >> >> > > -- > > * * > > * * > > * * > > *Quin Wills* > *DPhil candidate* > > * * > > *Department of Statistics* > > *University** of Oxford*** > > *1 South Parks Road* > *Oxford*** > > *OX1 3TG > United Kingdom* > > > > *01865 285 394* > -- ---------------------------------------------------------------- Steffen Durinck, PhD Division of Biostatistics, University of California, Berkeley & Life Sciences Department, Lawrence Berkeley National Laboratory 1 cyclotron Rd, Berkeley CA, 94720, USA Tel: +1-510-486-5202

Dear Quin, In general it is sufficient the send the same mail only once to this list, there is no added benefit in looping over the send button, and indeed might collect you bad karma from all the people who have to clean their mailboxes. The manual page of the "getGene" function says Usage: getGene( id, type, mart) Arguments: id: *vector* of gene identifiers one wants to annotate I am not sure how this could be more clear. R is a well-developed and powerful language and many people have benefited from reading introductions such as this one (on CRAN): http://www.stats.bris.ac.uk/R/doc/manuals/R-intro.html -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber 27/03/2008 18:19 Quin Wills a ?crit > Thank you Steffen for the really quick reply. > > Out of interest, I tried using Sys.sleep() but I still get the same > problem. www.ensembl.org is also running quite slowly this side for > queries, and I wonder if that might be somehow related. > > Sorry if this is in the manual - I didn't spot it. How many queries in a > batch do you think one should avoid going over? I've a fairly long list > of identifiers. > > Quin > > > Steffen wrote: >> Hi Quin, >> >> How long is your list of identifiers? It is not recommended to run a >> query like this in loops as this causes the web service to go out of >> sync at some point during the loop. >> biomaRt is made to perform batch queries. >> I would recommend to do your query as follows: >> >> genes <- getGene(id=ID, type="refseq_dna", mart=ensembl) >> >> This will give you a dataframe with the info for all the genes. If >> needed you can then loop over the result. >> If you feel like you really need to loop you could add Sys.sleep(1) >> in the loop. >> >> Cheers, >> Steffen >> >> Quin Wills wrote: >>> Hello all >>> >>> I'm running the most up to date R and biomaRt. >>> >>> I get the following error: >>> >Error: ncol(result) == length(attributes) is not TRUE >>> >>> for the following loop: >>> # 'ID' is a character vector of refseq IDs >>> #'gene', for the purposes of the argument here, is a list storing the >>> output >>> >>> > ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl") >>> > for (i in 1:length(ID)) { >>> > gene[[i]] <- getGene(id=ID[i], type="refseq_dna", mart=ensembl) >>> > } >>> >>> The problem is not dependent on the get function used or the id type >>> used. I didn't have this problem yesterday on the same script. The >>> error also occurs randomly, breaking the loop at any particular >>> point, sometimes allowing thousands of loops to run. >>> >>> Could this be a problem with the server I'm pulling the information >>> from? It just seems too random to be my coding - especially >>> considering I didn't have this problem yesterday. >>> >>> I've had this before, ages ago, and would like to get to the bottom >>> of it. And wisdom? Thanks. >>> >>> >>> * * >>> >>> * * >>> >>> * * >>> >>> *Quin Wills* >>> *DPhil candidate* >>> >>> * * >>> >>> *Department of Statistics* >>> >>> *University** of Oxford*** >>> >>> *1 South Parks Road* >>> *Oxford*** >>> >>> *OX1 3TG >>> United Kingdom* >>> >>> >>> >>> *01865 285 394* >>> >>> >>> [[alternative HTML version deleted]]