Great suggestions! Thanks! adding refseq as attributes too, why didn't I think of that? :-) Jose Quoting Steffen Durinck <durincks at="" mail.nih.gov="">: > Hi, > > I would like to add that biomaRt in RCurl mode can handle big queries > but will break when you use it in a big loop. > An alternative to what Jim suggests could be to do the query for all ids > at once: > > A<-getBM(attributes=c("hgnc_symbol","refseq_dna"),mart=mart,filters= "refseq_dna",values=RS) > > By adding refseq_dna as an attribute, HUGO symbols and RefSeq > identifiers will be automatically matched up in A. If needed, you > can loop over the result in A and you avoid doing 18000+ separate > database queries so it will be faster. > > best, > Steffen > > > > > James W. MacDonald wrote: >> J.delasHeras at ed.ac.uk wrote: >> >>> Hi, >>> >>> I suspect this is something to do purely with my connection, but I >>> thought I'd ask, just in case: >>> >>> I have a list of refseq ids (NM_xxxxx), 18028 of them. >>> I wanted to get the gene symbols for those genes, so I used biomaRt >>> on the whole list. What I got was a single column data frame longer >>> than 18028, as I get multiple results with some of these refseq >>> ids. There doesn't seem to be an easy way to regroup them together, >>> so I do the following instead: >>> >> >> Using the RCurl interface for a big query like that isn't ideal. You >> would be better off installing RMySQL and using the MySQL interface >> (note: you can get RMySQL using biocLite(), thanks to the fine folks >> in Seattle). Also, you can have getBM() put things in a list, so any >> duplicated gene symbols will be grouped together. >> >> A <- getBM("hgnc_symbol", "refseq_dna", RS, mart = mart, output = >> "list", mysql = TRUE) >> >> Should do the trick. >> >> HTH, >> >> Jim >> >> >> >>> #create an empty list of teh right length >>> A<-vector(mode="list", length=18028) >>> #now loop filling elements of the list from the biomaRt queries >>> for (i in 1:18028){ >>> K<-i >>> A[[i]]<-getBM(attributes=c("hgnc_symbol"),mart=mart,filters="refse q_dna",values=c(RS[i])) >>> } >>> print(K) >>> >>> RS is a vector containing the 18028 refseq ids. >>> the K value is only so that I know where it breaks... because >>> that's what happens... after a while, it breaks with an error >>> message: >>> >>> Error in postForm(paste(mart at host, "?", sep = ""), query = xmlQuery) : >>> couldn't connect to host >>> >>> This doesn't happen if I send the whole query in ONE go, in a >>> vector... but if I do it element by element it breaks after 3-4000 >>> queries. >>> Any ideas to do this in a simpler/better way? Or at least one that >>> doesn't have me coming back to re-start the loop at the position of >>> the last break? >>> >>> thanks! >>> >>> Jose >>> >>> >> >> >> > > > -- > Steffen Durinck, Ph.D. > > Oncogenomics Section > Pediatric Oncology Branch > National Cancer Institute, National Institutes of Health > URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ > > Phone: 301-402-8103 > Address: > Advanced Technology Center, > 8717 Grovemont Circle > Gaithersburg, MD 20877 > -- Dr. Jose I. de las Heras Email: J.delasHeras at ed.ac.uk The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131 6513374 Institute for Cell & Molecular Biology Fax: +44 (0)131 6507360 Swann Building, Mayfield Road University of Edinburgh Edinburgh EH9 3JR UK