[BioC] error message about makeTranscript funciton in package GenomeGraphs

[Steffen at stat.Berkeley.EDU]

Hi Shirley,

It looks like your version of GenomeGraphs is too old.  Update
GenomeGraphs to a version of 1.4.0 or higher and this example should work
again.

Cheers,
Steffen

> Dear List,
>
> When I tried to run examples in  the user guide of package
> "GenomeGraphs", I got the following error message
> after coping the code on page 3.  The code on page 2
> "gdPlot(gene)"works fine.
>
>> transcript <- makeTranscript(id = "ENSG00000095203", type =
>> "ensembl_gene_id", biomart = mart)
> Error in getBM(c("structure_gene_stable_id",
> "structure_transcript_stable_id",  :
>  Invalid attribute(s): structure_gene_stable_id,
> structure_transcript_stable_id
> Please use the function 'listAttributes' to get valid attribute names
>
> Can anybody kindly tell me what I am missing? Thanks.
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.iso885915;LC_NUMERIC=C;LC_TIME=en_US.iso885915;LC_COLLATE=en_US.iso885915;LC_MONETARY=C;LC_MESSAGES=en_US.iso885915;LC_PAPER=en_US.iso885915;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.iso885915;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] GenomeGraphs_1.2.3 biomaRt_2.0.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.3-0
>
>
> --
> Xiaoling
>
> _______________________________________________
> 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
>