Agreed -- I didn't realize that all these fields were being auto-discovered. Maybe we should instead be able to instruct getBM() about field types, just as we already do with scan() and friends. -Aaron On Thu, Dec 3, 2009 at 9:29 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > > > Aaron Mackey wrote: > >> I would expect that identifiers be treated as strings, not integers (even >> if an identifier happened to look like an integer most of the time -- it's >> not guaranteed to be true forever), no? We don't do any math on the >> identifiers, so why cast them to integers? >> > > I would think this is another maintenance issue, although I don't presume > to speak for Steffen on why things work as they do. But think for a moment > about what you are asking. > > The getBM() function is an all-purpose query device intended to get stuff > from a database. Some of this stuff is numeric, and some of it is character. > Some of the stuff that might be better treated as character looks like it is > integer. > > There are multiple different Biomart servers that can be queried using > getBM(): > > > listMarts() > biomart > 1 ensembl > 2 snp > 3 functional_genomics > 4 vega > 5 msd > 6 bacterial_mart_3 > 7 fungal_mart_3 > 8 metazoa_mart_3 > 9 plant_mart_3 > 10 protist_mart_3 > 11 htgt > 12 REACTOME > 13 wormbase_current > 14 dicty > 15 rgd__mart > 16 ipi_rat__mart > 17 SSLP__mart > 18 g4public > 19 pride > 20 intermart-1 > 21 uniprot_mart > 22 ensembl_expressionmart_48 > 23 biomartDB > 24 Eurexpress Biomart > 25 pepseekerGOLD_mart06 > 26 Potato_01 > 27 Sweetpotato_01 > 28 Pancreatic_Expression > 29 ENSEMBL_MART_ENSEMBL > 30 GRAMENE_MARKER_30 > 31 GRAMENE_MAP_30 > 32 QTL_MART > > not to mention the archived Biomart servers that can be queried. > > So what you are asking is for Steffen to go through all those databases, > look for all the data that appear to be integer, but should be kept as > character, and then set up some functionality to make sure this happens. > > In addition, he would then need to maintain this over time as different > data are added to the various Biomart servers that can be queried (and as > new Biomart servers come on line). > > Sounds like fun to me! > > Best, > > Jim > > > >> -Aaron >> >> On Wed, Dec 2, 2009 at 10:38 AM, James W. MacDonald < >> jmacdon@med.umich.edu <mailto:jmacdon@med.umich.edu>> wrote: >> >> >> >> Tereza Roca wrote: >> >> thank you. this is bizarre... but now it works... >> shouldn't this be fixed so that output of your query agrees with >> the input you have to provide for the query? >> >> >> Theoretically, yes. However it would be more difficult than you >> would think. Note that R automatically truncates leading zeros: >> >> > 0002350152 >> [1] 2350152 >> >> So when the Biomart server returns the Illumina ID (as a number), R >> automatically truncates the leading zeros. One could use sprintf() >> to keep the leading zeros, but you have to know a priori the width >> of the field: >> >> > sprintf("%010d", 0002350152) >> [1] "0002350152" >> >> There may be a trick to check the number of digits for a number >> prior to R truncating leading zeros, but if there is one, I don't >> know what it would be. If not, you would have to hard code the above >> sprintf() call to use 10 digits, assuming that all Illumina IDs have >> 10 digits. But what if not all Illumina IDs are 10 digits? What if >> they change to 7 digits in a future chip? >> >> As you can imagine, hard coding things like this can lead to a >> nightmare for the maintainer. So although this isn't an ideal >> situation I can't imagine things will change. >> >> Best, >> >> Jim >> >> >> >> >> >> >> >> ------------------------------------------------------------------ ------ >> *From:* James W. MacDonald <jmacdon@med.umich.edu>> <mailto:jmacdon@med.umich.edu>> >> *To:* Tereza Roca <rocatereza@yahoo.co.uk>> <mailto:rocatereza@yahoo.co.uk>> >> *Cc:* bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> >> *Sent:* Wed, 2 December, 2009 14:41:50 >> *Subject:* Re: [BioC] help with biomart >> >> Hi Tereza, >> >> >> Tereza Roca wrote: >> > I found something wrong with biomart: if I request an >> illumina ID from an esembl gene ID I obtain the following: >> >> getBM(attributes = >> c("ensembl_gene_id","illumina_humanwg_6_v1"), >> filters="ensembl_gene_id", values = "ENSG00000165891", mart = >> ensembl) >> > ensembl_gene_id illumina_humanwg_6_v1 >> > 1 ENSG00000165891 NA >> > 2 ENSG00000165891 2350152 >> > >> > this is fine (altough why is there a NA?) >> > >> > but if I request the contrary (from illumina to gene ID) I >> don't obtain anything: >> > >> >> getBM(attributes = >> c("illumina_humanwg_6_v1","ensembl_gene_id"), >> filters="illumina_humanwg_6_v1", values = c("2350152"), mart = >> ensembl) >> > [1] illumina_humanwg_6_v1 ensembl_gene_id <0 rows> (or >> 0-length row.names) >> > >> > is this an error? or am I making some mistakes in the way I >> request it? Please advice >> >> Well, you aren't doing the correct query, but I don't know if I >> would call it a mistake (or a weird 'feature' of how Illumina >> IDs are coded in the Biomart database). I figured this out by >> doing your first query at the Biomart server, which returned >> 0002350152 for the Illumina ID. >> >> > getBM(attributes = >> c("illumina_humanwg_6_v1","ensembl_gene_id"), >> filters="illumina_humanwg_6_v1", "0002350152",mart) >> illumina_humanwg_6_v1 ensembl_gene_id >> 1 2350152 ENSG00000165891 >> >> >> Best, >> >> Jim >> >> >> >> >> > >> > thank you >> > >> > Tereza >> > >> > >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@stat.math.ethz.ch >> <mailto:bioconductor@stat.math.ethz.ch> >> <mailto:bioconductor@stat.math.ethz.ch>> <mailto:bioconductor@stat.math.ethz.ch>> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> -- James W. MacDonald, M..S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and >> should not be used for urgent or sensitive issues >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> _______________________________________________ >> >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch <mailto:bioconductor@stat.math.ethz.ch> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]