[Bioc-devel] GenomicFeatures makeTranscriptDbFromUCSC Table Missing

[Hervé Pagès]

Hi Dario,

This problem is finally fixed in release (GenomicFeatures 1.4.5) and
devel (GenomicFeatures 1.5.28). It was caused by a db schema change
on UCSC side. Sorry again for the delay.

H.


On 11-10-07 11:20 AM, Hervé Pagès wrote:
> 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