Hi, I'm trying out the biomaRt package, but I am unable to reproduce the examples in the vignette. I get no error messages, but I do not get the correct output either. The functions getGO, getFeature, getHomolog, getGene, getOMIM and getXref all give empty output (as for getGO below). Only getSNP seems to work correctly. Session info below. Does anyone know what could be the matter here? Jelle > library(biomaRt) Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type: openVignette() For details on reading vignettes, see the openVignette help page. Loading required package: RMySQL Loading required package: DBI Warning message: DLL attempted to change FPU control word from 8001f to 9001f > mart <- martConnect() - Connected to: ensembl_mart_33 - - Connected to: vega_mart_33 - - Connected to: snp_mart_33 - - Connected to: sequence_mart_33 - > > getGO(id = "1939_at", array = "hg_u95av2", mart = mart) An object of class "martTable" Slot "id": [1] "1939_at" Slot "table": $GOID [1] NA $description [1] NA $evidence [1] NA $martID [1] NA > mart An object of class "Mart" Slot "ensembl": <mysqlconnection:(2608,1)> Slot "vega": <mysqlconnection:(2608,2)> Slot "sequence": <mysqlconnection:(2608,3)> Slot "snp": <mysqlconnection:(2608,4)> Slot "arrayToSpecies": V1 V2 1 canine cfamiliaris 2 drosgenome1 dmelanogaster 3 drosophila_2 dmelanogaster 4 zebrafish drerio 5 chicken ggallus 6 hc_g110 hsapiens 7 hg_focus hsapiens 8 hg_u133_plus_2 hsapiens 9 hg_u133a_2 hsapiens 10 hg_u133a hsapiens 11 hg_u133b hsapiens 12 hg_u95av2 hsapiens 13 hg_u95b hsapiens 14 hg_u95c hsapiens 15 hg_u95d hsapiens 16 hg_u95e hsapiens 17 hugenefl hsapiens 18 u133_x3p hsapiens 19 mg_u74av2 mmusculus 20 mg_u74bv2 mmusculus 21 mg_u74cv2 mmusculus 22 mouse430_2 mmusculus 23 mouse430a_2 mmusculus 24 rat230_2 rnorvegicus 25 rg_u34a rnorvegicus 26 rg_u34b rnorvegicus 27 rg_u34c rnorvegicus > sessionInfo() R version 2.1.0, 2005-04-18, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: biomaRt RMySQL DBI Biobase "1.0.4" "0.5-6" "0.1-9" "1.5.12"

Hi Jelle, The problem is that you are using an old version of biomaRt. Everything will work if you use the biomaRt version 1.2.2 which is available from the developmental packages webpage. best, Steffen Goeman, J.J. (MSTAT) wrote: > Hi, > >I'm trying out the biomaRt package, but I am unable to reproduce the examples in the vignette. I get no error messages, but I do not get the correct output either. The functions getGO, getFeature, getHomolog, getGene, getOMIM and getXref all give empty output (as for getGO below). Only getSNP seems to work correctly. Session info below. > >Does anyone know what could be the matter here? > >Jelle > > > > > >>library(biomaRt) >> >> >Loading required package: Biobase >Loading required package: tools >Welcome to Bioconductor > Vignettes contain introductory material. To view, > simply type: openVignette() > For details on reading vignettes, see > the openVignette help page. >Loading required package: RMySQL >Loading required package: DBI >Warning message: >DLL attempted to change FPU control word from 8001f to 9001f > > >>mart <- martConnect() >> >> >- Connected to: ensembl_mart_33 - >- Connected to: vega_mart_33 - >- Connected to: snp_mart_33 - >- Connected to: sequence_mart_33 - > > >>getGO(id = "1939_at", array = "hg_u95av2", mart = mart) >> >> >An object of class "martTable" >Slot "id": >[1] "1939_at" > >Slot "table": >$GOID >[1] NA > >$description >[1] NA > >$evidence >[1] NA > >$martID >[1] NA > > > > >>mart >> >> >An object of class "Mart" >Slot "ensembl": ><mysqlconnection:(2608,1)> > >Slot "vega": ><mysqlconnection:(2608,2)> > >Slot "sequence": ><mysqlconnection:(2608,3)> > >Slot "snp": ><mysqlconnection:(2608,4)> > >Slot "arrayToSpecies": > V1 V2 >1 canine cfamiliaris >2 drosgenome1 dmelanogaster >3 drosophila_2 dmelanogaster >4 zebrafish drerio >5 chicken ggallus >6 hc_g110 hsapiens >7 hg_focus hsapiens >8 hg_u133_plus_2 hsapiens >9 hg_u133a_2 hsapiens >10 hg_u133a hsapiens >11 hg_u133b hsapiens >12 hg_u95av2 hsapiens >13 hg_u95b hsapiens >14 hg_u95c hsapiens >15 hg_u95d hsapiens >16 hg_u95e hsapiens >17 hugenefl hsapiens >18 u133_x3p hsapiens >19 mg_u74av2 mmusculus >20 mg_u74bv2 mmusculus >21 mg_u74cv2 mmusculus >22 mouse430_2 mmusculus >23 mouse430a_2 mmusculus >24 rat230_2 rnorvegicus >25 rg_u34a rnorvegicus >26 rg_u34b rnorvegicus >27 rg_u34c rnorvegicus > > > >>sessionInfo() >> >> >R version 2.1.0, 2005-04-18, i386-pc-mingw32 > >attached base packages: >[1] "tools" "methods" "stats" "graphics" "grDevices" "utils" >[7] "datasets" "base" > >other attached packages: > biomaRt RMySQL DBI Biobase > "1.0.4" "0.5-6" "0.1-9" "1.5.12" > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor > > >