biomaRt issues
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@lcolladotor
Last seen 7 days ago
United States
Hello BioC users :) I'm having some trouble with biomaRt with the uniprot database. #I can execute the following code and everything works fine (with ENSEMBL): library(biomaRt) bsub <- useMart( "bacterial_mart_54", dataset = "bac_6_gene") res <- getBM( attributes=c("start_position", "end_position", "strand", "status"), filters= c("start", "end"), values = list("1", "100000"), mart = bsub) library(lattice) print(xyplot(end_position~start_position | status, group=strand, data=res, auto.key=TRUE)) #But then, if I want to retrieve the EC numbers and organism info for the viral proteins on Uniprot, this should work: # (I did it first through http://www.ebi.ac.uk/uniprot/biomart/martview and it worked) library(biomaRt) uni <- useMart("uniprot_mart", dataset="UNIPROT") virus <- getBM(attributes = c("ec_number","organism"), filters = "superregnum_name", values = "Viruses", mart = uni) dim(virus) [1] 0 2 # But the virus object has 0 rows. The same happens if I use checkFilters = FALSE # Using the website app, I do get information back. # If I check only the "organism" attribute, then I do get some information. virus2 <- getBM(attributes = c("organism"), filters = "superregnum_name", values = "Viruses", mart = uni) dim(virus2) [1] 5063 1 # However, I re did the "virus2" object a few minutes later and got a different result (I checked around 4 times and got the same numbers): virus2 <- getBM(attributes = c("organism"), filters = "superregnum_name", values = "Viruses", mart=uni) dim(virus2) [1] 158 1 # Then once more after I typed the above lines on this mail, and I got the same original result virus2 <- getBM(attributes = c("organism"), filters = "superregnum_name", values = "Viruses", mart=uni) dim(virus2) [1] 5063 1 # I'm pretty sure that I didn't lose my internet connection on the meantime, so I don't really know what is causing this error. # I then tried the same lines on a different machine (different network too) and at first I got the same 5063 row value, and then I got: virus2 <- getBM(attributes = c("organism"), filters = "superregnum_name", values = "Viruses", mart=uni) dim(virus2) [1] 8431 1 # Then 5063 again, etc. In the end, 5063 seems to pop up more frequently, but is it the actual result? Is there a way to make sure I'm not missing information without calling getBM multiple times to check that there are no unexpected results? I had assigned some homework exercises using biomaRt to access Uniprot, but now I'm confused myself about what's going on :P Any tips will be great :) Thanks! Leonardo # First comp session info sessionInfo() R version 2.10.0 Under development (unstable) (2009-07-21 r48968) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lattice_0.17-25 biomaRt_2.1.0 loaded via a namespace (and not attached): [1] grid_2.10.0 RCurl_0.98-1 XML_2.5-1 # Second comp session info sessionInfo() R version 2.10.0 Under development (unstable) (2009-08-10 r49131) sparc-sun-solaris2.9 locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.1.0 loaded via a namespace (and not attached): [1] RCurl_1.2-0 XML_2.6-0 -- Leonardo Collado Torres, Bachelor in Genomic Sciences Professor at LCG and member of Dr. Enrique Morett's lab UNAM Campus Cuernavaca, Mexico Homepage: http://www.lcg.unam.mx/~lcollado/ Phone: [52] (777) 313-28-05
Organism biomaRt Organism biomaRt • 1.2k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Leonardo Thank you for your clear and helpful problem report! The lack of returned results (in one case), and the irreproducibility of returned results (in another case) seem to be a problem of the UniProt mart rather than of the biomaRt package per se. I cc Jie Luo at EBI who, afaIu, would be the most appropriate person to respond here, and perhaps help to localise and eliminate the problem. Best wishes Wolfgang Leonardo Collado Torres ha scritto: > Hello BioC users :) > > I'm having some trouble with biomaRt with the uniprot database. > > #I can execute the following code and everything works fine (with ENSEMBL): > library(biomaRt) > bsub <- useMart( "bacterial_mart_54", dataset = "bac_6_gene") > res <- getBM( attributes=c("start_position", "end_position", "strand", > "status"), filters= c("start", "end"), values = list("1", "100000"), > mart = bsub) > library(lattice) > print(xyplot(end_position~start_position | status, group=strand, > data=res, auto.key=TRUE)) > > #But then, if I want to retrieve the EC numbers and organism info for > the viral proteins on Uniprot, this should work: > # (I did it first through http://www.ebi.ac.uk/uniprot/biomart/martview > and it worked) > library(biomaRt) > uni <- useMart("uniprot_mart", dataset="UNIPROT") > virus <- getBM(attributes = c("ec_number","organism"), filters = > "superregnum_name", values = "Viruses", mart = uni) > dim(virus) > [1] 0 2 > # But the virus object has 0 rows. The same happens if I use > checkFilters = FALSE > # Using the website app, I do get information back. > # If I check only the "organism" attribute, then I do get some information. > virus2 <- getBM(attributes = c("organism"), filters = > "superregnum_name", values = "Viruses", mart = uni) > dim(virus2) > [1] 5063 1 > # However, I re did the "virus2" object a few minutes later and got a > different result (I checked around 4 times and got the same numbers): > virus2 <- getBM(attributes = c("organism"), filters = > "superregnum_name", values = "Viruses", mart=uni) > dim(virus2) > [1] 158 1 > # Then once more after I typed the above lines on this mail, and I got > the same original result > virus2 <- getBM(attributes = c("organism"), filters = > "superregnum_name", values = "Viruses", mart=uni) > dim(virus2) > [1] 5063 1 > # I'm pretty sure that I didn't lose my internet connection on the > meantime, so I don't really know what is causing this error. > # I then tried the same lines on a different machine (different network > too) and at first I got the same 5063 row value, and then I got: > virus2 <- getBM(attributes = c("organism"), filters = > "superregnum_name", values = "Viruses", mart=uni) > dim(virus2) > [1] 8431 1 > # Then 5063 again, etc. > > In the end, 5063 seems to pop up more frequently, but is it the actual > result? Is there a way to make sure I'm not missing information without > calling getBM multiple times to check that there are no unexpected results? > I had assigned some homework exercises using biomaRt to access Uniprot, > but now I'm confused myself about what's going on :P > Any tips will be great :) Thanks! > > Leonardo > > > # First comp session info > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-07-21 r48968) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 [3] LC_MONETARY=English_United States.1252 > LC_NUMERIC=C [5] LC_TIME=English_United > States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] lattice_0.17-25 biomaRt_2.1.0 > loaded via a namespace (and not attached): > [1] grid_2.10.0 RCurl_0.98-1 XML_2.5-1 > # Second comp session info > sessionInfo() > R version 2.10.0 Under development (unstable) (2009-08-10 r49131) > sparc-sun-solaris2.9 > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.1.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.2-0 XML_2.6-0 > -- Best wishes Wolfgang ------------------------------------------------------- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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