[Bioc-devel] GenomicFeatures makeTranscriptDbFromUCSC Table Missing

[Hervé Pagès]

Hi Dario,

Sorry that I didn't see your email earlier. Thanks for the report.
We also have this problem here:

 
http://bioconductor.org/checkResults/2.8/bioc-LATEST/GenomicFeatures/lamb1-checksrc.html

I'm currently looking at this. Will come back soon.

H.


On 11-09-13 08:00 PM, Dario Strbenac wrote:
> Hello,
>
> I noticed that getting an ENSEMBL gene table for the hg18 assembly doesn't work
>
>> hg18Ens<- makeTranscriptDbFromUCSC(genome="hg18",tablename="ensGene")
> Download the ensGene table ... OK
> Download the ensGtp table ... Error in normArgTable(value, x) : unknown table name 'ensGtp'
>
> but for hg19 it does.
>
> makeTranscriptDbFromUCSC(genome="hg19",tablename="ensGene")
> Download the ensGene table ... OK
> Download the ensGtp table ... OK
> Extract the 'transcripts' data frame ... OK
> Extract the 'splicings' data frame ... OK
> Download and preprocess the 'chrominfo' data frame ... OK
> Prepare the 'metadata' data frame ... OK
> Make the TranscriptDb object ... OK
>
> I can download ensGtp hg18 manually from the UCSC website.
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319