Hello everyone, Ill be blunt: I want to make multiple queries with the getGene funciton of biomaRt, but having some trouble (this is probably my lack of knowledge in programming) first I make an object containing 3 entrez gene ID's. test=c("4205","9185","4791") if i then library(biomaRt) mart <- martConnect( biomarts = c("ensembl","vega")) g= getGene( id = test[1], type = "entrezgene", species = "hsapiens", db = "ensembl", mart = mart) g This workes. But I want to make a "for loop", so that getGene retrieves all my 3 id's in one go.. ive tried several "for loops", but I think I have trouble handeling the returning martTable-class. So my question is: Have anyone else managed to build a "for loop" of getGene, and is it doable with the returning martTable-class ? best morten

On 12/15/05 7:37 AM, "Morten Mattingsdal" <morten.mattingsdal at="" student.uib.no=""> wrote: > This workes. But I want to make a "for loop", so that getGene retrieves > all my 3 id's in one go.. ive tried several "for loops", but I think I > have trouble handeling the returning martTable-class. > > So my question is: > Have anyone else managed to build a "for loop" of getGene, and is it > doable with the returning martTable-class ? You don't need to do a "for loop". This works: g <- getGene(id=test, type="entrezgene", species="hsapiens", db="ensembl", mart=mart)

Hi Morton, The getGene function works with a list of id's so you could do: test=c("4205","9185","4791") g= getGene( id = test, type = "entrezgene", species = "hsapiens", mart = mart) Thus without a loop. Including a loop to do this is not recommended as this will slow down the data retrieval. Entering a list results in just one fast query. The default output of the getGene function has recently changed to a data.frame which is easier to work with then a martTable. If you enter a list of id's, the getGene function will now return a data.frame with and id per row. Make sure you work with the latest biomaRt version (1.5.2) downloadable from the 1.8 developmental packages page. best, Steffen > Hello everyone, > Ill be blunt: I want to make multiple queries with the getGene funciton > of biomaRt, but having some trouble (this is probably my lack of > knowledge in programming) > > first I make an object containing 3 entrez gene ID's. > > test=c("4205","9185","4791") > > if i then > > library(biomaRt) > mart <- martConnect( biomarts = c("ensembl","vega")) > g= getGene( id = test[1], type = "entrezgene", species = "hsapiens", db > = "ensembl", mart = mart) > g > > This workes. But I want to make a "for loop", so that getGene retrieves > all my 3 id's in one go.. ive tried several "for loops", but I think I > have trouble handeling the returning martTable-class. > > So my question is: > Have anyone else managed to build a "for loop" of getGene, and is it > doable with the returning martTable-class ? > > best > morten > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >