Thanks a lot to everybody who replied! I see that this is a problem for now, but it is being dealt with, which is good. Cheers, Sergei Steffen wrote: > Hi Sergei, > > The Ensembl team has been contacted about the loss of markersymbol as > filter and attribute in the latest release of the Ensembl BioMart. > It looks like this was not intended and they will put the markersymbol > attribute/filter back. They are planning to put them in next Wednesday > and then the Ensembl webteam will have to propagate this fix across > the machines. > > We'll have to use Marc's workaround in the meantime. > > Cheers, > Steffen > > Marc Carlson wrote: >> Siarhei Manakou wrote: >> >>> Hello, >>> >>> I am accessing biomarts through bioconductor. It used to be possible >>> to use list of gene symbols and retrieve pretty much what you wanted >>> using getBM() function and specifying "markersymbol" as filters. Now >>> this thing doesn't work anymore. I know that in order to retrieve >>> gene symbols from, let's say, ensembl geneIDs - you can specify >>> "external_gene_id", as attributes and you will get your list of gene >>> symbols. However things don't work other way around and putting >>> "external_gene_id" as filters doesn't work. So do you know how it is >>> possible to use gene symbols these days in order to retrieve >>> information from biomarts? >>> >>> thanks, >>> Sergei >>> >>> >>> >> It occurs to me that you might be able to use the latest bioconductor >> annotation packages to work around this. You could use an organism >> based package to map from gene symbols over to entrez gene IDs for >> instance. Then you could just feed those IDs into biomart instead as a >> work around. >> >> So something like: >> >> library("org.Hs.eg.db") >> foo <- c("GLP-1","HOTAIR","SCARNA27") >> mget(foo,envir=org.Hs.egSYMBOL2EG) >> >> >> Marc >> >> _______________________________________________ >> 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 >> >> -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.