Question

problems with GenomeGraphs

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steffen@stat.Berkeley.EDU ▴ 600

@steffenstatberkeleyedu-2907

Last seen 10.2 years ago

Hi Raphael, I week ago there was an new release of Ensembl and a few of attributes in Ensembl changed names. These changes have been fixed in the GenomeGraphs package available here: http://bioconductor.org/packages/2.3/bioc/html/GenomeGraphs.html Cheers, Steffen > Hi Jim and Steffen, > > I have been trying to use your package GenomeGraphs, but I get the > following error when I tried the following code in the vignette: > > mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > Checking attributes and filters ... ok > > gene = new("Gene", id = "ENSG00000095203", type = > "ensembl_gene_id", biomart = mart) > Error in getBM(c("structure_gene_stable_id", > "structure_transcript_stable_id", : > Invalid attribute(s): structure_exon_stable_id, > structure_exon_chrom_start, structure_exon_chrom_end, > structure_exon_rank > Please use the function 'listAttributes' to get valid attribute names > > > > For you information, I use R 2.7 (64bit) on a OS X Leopard. Could you > please let me know what I am doing wrong? > > Thanks! > > Raphael >

biomaRt GenomeGraphs biomaRt GenomeGraphs • 996 views

ADD COMMENT • link updated 16.3 years ago by Steve Lianoglou ★ 13k • written 16.3 years ago by steffen@stat.Berkeley.EDU ▴ 600

score 0 · Answer 1 · 2008-08-04

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 20 months ago

United States

Hi, On Aug 4, 2008, at 2:42 PM, steffen at stat.berkeley.edu wrote: > Hi Raphael, > > I week ago there was an new release of Ensembl and a few of > attributes in > Ensembl changed names. These changes have been fixed in the > GenomeGraphs > package available here: > > http://bioconductor.org/packages/2.3/bioc/html/GenomeGraphs.html What's the best way to install this, assuming we're using R 2.7.x and, therefore, pulling from the BioC 2.2 repos (by default)? Do we have to update to R 2.8-devel, or should we just try to download the binary from that webpage and install manually? -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College of Cornell University http://cbio.mskcc.org/~lianos

ADD COMMENT • link 16.3 years ago Steve Lianoglou ★ 13k

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On Aug 4, 2008, at 5:50 PM, Steve Lianoglou wrote: > Hi, > > On Aug 4, 2008, at 2:42 PM, steffen at stat.berkeley.edu wrote: > >> Hi Raphael, >> >> I week ago there was an new release of Ensembl and a few of >> attributes in >> Ensembl changed names. These changes have been fixed in the >> GenomeGraphs >> package available here: >> >> http://bioconductor.org/packages/2.3/bioc/html/GenomeGraphs.html > > What's the best way to install this, assuming we're using R 2.7.x > and, therefore, pulling from the BioC 2.2 repos (by default)? > > Do we have to update to R 2.8-devel, or should we just try to > download the binary from that webpage and install manually? To answer my own question ... I just downloaded the source from the BioC 2.3 repo and did a round of $ R CMD build GenomeGraphs $ R CMD install GenomeGraphs_1.1.2.tar.gz And things seem to be working so far in my R 2.7.1/BioC 2.2 environment (I already had the dependencies installed). -steve -- Steve Lianoglou Graduate Student: Physiology, Biophysics and Systems Biology Weill Cornell Medical College of Cornell University http://cbio.mskcc.org/~lianos

ADD REPLY • link 16.3 years ago Steve Lianoglou ★ 13k