Hi Mayte, You have uncovered a bug in probes2tableBM(). I will fix this in the devel version. I am in the process of setting up a new work computer, so I am not able to check things out right now - when I am able I will see if there is a quick workaround that will get you going right now. Best, Jim Steffen wrote: > Hi Mayte, > > The hgu133a2 chip has a different attribute and filter name in Ensembl > and it looks like the probes2tableBM function assumes that the filter > and attribute names are the same for every platform (ideally it should). > The attribute name for this platform is affy_hg_u133a_v2 and the filter > name is affy_hg_u133a_2. Maybe Jim can comment on how to get the > function working in this case? > Alternatively you can do your query using the getBM function instead of > probes2tableBM. > > Cheers, > Steffen > > > Mayte Suarez-Farinas wrote: >> Hi, >> >> I am having problems with function probes2tableBM again, and I can >> not figure it out what is the right >> ann.source for hgu133a2 chips. here is the code >> >> >> > mart_hs=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") >> Checking attributes and filters ... ok >> >> > probes2tableBM(eset, probids=featureNames(eset) >> [1:10],filename='llll', >> + species="hsapiens", >> ann.source="affy_hg_u133a_2", links=linksBM()[c(1:3)], otherann=annBM >> ()[1:2], affyid=TRUE, express=FALSE) >> connected to: ensembl >> Reading database configuration of: hsapiens_gene_ensembl >> Checking attributes and filters ... ok >> Checking main tables ... ok >> Error in getBM(attributes = links$links, filter = ann.source, values >> = gn, : >> Invalid attribute(s): affy_hg_u133a_2 >> Please use the function 'listAttributes' to get valid attribute names >> >> >> when I do that: >> >> > listAttributes(mart_hs)[1:20,] >> name description >> 1 affy_hcg110 AFFY HCG110 >> 2 affy_hg_focus AFFY HG FOCUS >> 3 affy_hg_u133_plus_2 AFFY HG U133-PLUS-2 >> 4 affy_hg_u133a AFFY HG U133A >> 5 affy_hg_u133a_v2 AFFY HG U133Av2 >> 6 affy_hg_u133b AFFY HG U133B >> 7 affy_hg_u95a AFFY HG U95A >> 8 affy_hg_u95av2 AFFY HG U95AV2 >> 9 affy_hg_u95b AFFY HG U95B >> 10 affy_hg_u95c AFFY HG U95C >> 11 affy_hg_u95d AFFY HG U95D >> 12 affy_hg_u95e AFFY HG U95E >> 13 affy_hugenefl AFFY HUGENEFL >> 14 affy_u133_x3p AFFY U133 X3P >> 15 agilent_cgh Agilent cgh >> 16 agilent_probe Agilent Probe >> 17 band Band >> 18 biotype Biotype >> 19 ccds CCDS ID >> 20 chromosome_name Chromosome Name >> >> >> >> so I tried with ann.source=affy_hg_u133a_v2 but I get another error: >> >> > probes2tableBM(eset, probids=featureNames(eset) >> [1:10],filename='llll', >> + species="hsapiens", >> ann.source="affy_hg_u133a_v2", links=linksBM()[c(1:3)], otherann=annBM >> ()[1:2], affyid=TRUE, express=FALSE) >> connected to: ensembl >> Reading database configuration of: hsapiens_gene_ensembl >> Checking attributes and filters ... ok >> Checking main tables ... ok >> Error: ' affy_hg_u133a_v2 'is not an available annotation source for >> this biomaRt or this species. >> Available choices are listed below: >> name >> description >> 1 affy_hc_g110 Affy hc g 110 >> ID(s) >> 2 affy_hg_focus Affy hg focus >> ID(s) >> 3 affy_hg_u133_plus_2 Affy hg u133 plus 2 >> ID(s) >> 4 affy_hg_u133a Affy hg u133a >> ID(s) >> 5 affy_hg_u133a_2 Affy hg u133a 2 >> ID(s) >> 6 affy_hg_u133b Affy hg u133b >> ID(s) >> 7 affy_hg_u95a Affy hg u95a >> ID(s) >> 8 affy_hg_u95av2 Affy hg u95av2 >> ID(s) >> 9 affy_hg_u95b Affy hg u95b >> ID(s) >> 10 affy_hg_u95c Affy hg u95c >> ID(s) >> 11 affy_hg_u95d Affy hg u95d >> ID(s) >> 12 affy_hg_u95e Affy hg u95e >> ID(s) >> 13 affy_hugenefl Affy hugenefl >> ID(s) >> 14 affy_u133_x3p Affy u133 x3p >> ID(s) >> ............ >> >> >> >> sessionInfo() >> R version 2.5.0 (2007-04-23) >> i386-apple-darwin8.9.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" >> "utils" "datasets" "methods" "base" >> >> other attached packages: >> RMySQL DBI affycoretools annaffy >> xtable gcrma matchprobes biomaRt RCurl >> "0.5-11" "0.2-2" "1.8.0" "1.8.1" >> "1.4-3" "2.8.0" "1.8.1" "1.10.0" "0.8-0" >> XML GOstats Category Matrix >> lattice genefilter survival KEGG RBGL >> "1.7-3" "2.2.1" "2.2.1" "0.9975-11" >> "0.15-4" "1.14.1" "2.31" "1.15.13" "1.12.0" >> annotate GO graph limma >> affy affyio Biobase >> "1.14.1" "1.16.0" "1.14.0" "2.10.0" >> "1.14.0" "1.4.0" "1.14.0" >> >> _______________________________________________ >> 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 >> >> > > _______________________________________________ > 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