Hi Jim,

Thanks for the reply. Yes, I am running this on Windows. I followed your
suggestion to use setInternet2() function first, but I still get an error:

> setInternet2()
> txdb <- makeTranscriptDbFromUCSC(genome='hg19',tablename='ensGene')
Error in function (type, msg, asError = TRUE)  : couldn't connect to host

I also tried:

> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0.
Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene'
trying URL '
http://bioconductor.org/packages/2.14/data/annotation/bin/windows/contrib/3.1/TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0.zip
'
Content type 'application/zip' length 18546564 bytes (17.7 Mb)
opened URL
downloaded 17.7 Mb

How do I read this table "TxDb.Hsapiens.UCSC.hg19.knownGene"? Also, is
there documentation on the differences between "knownGene" and "ensGene"?

Thanks for helping.
Sharvari




On Tue, Jun 17, 2014 at 12:39 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Sharvari,
>
>
> On 6/17/2014 10:56 AM, Sharvari.Gujja@sanofi.com wrote:
>
>> Hi Steve,
>>
>>
>> I get the same error trying to run txdb <- makeTranscriptDbFromUCSC(
>> genome='hg19',tablename='knownGene')
>>
>> Error in function (type, msg, asError = TRUE)  : couldn't connect to host
>>
>
> This error means you are not able to connect to UCSC. This may be due to
> an intermittent outage on their end, or possibly because you are behind a
> firewall.
>
> But note that if you want the knownGene transcript package, you can get
> that from Bioconductor without having to build it yourself:
>
> library(BiocInstaller)
> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
>
> If you want the ensGene table you will have to build that one yourself. I
> just tried that using your code, and it works for me:
>
>
> > txdb <- makeTranscriptDbFromUCSC(genome='hg19',tablename='ensGene')
> Download the ensGene 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
> Warning message:
> In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :
>   UCSC data anomaly in 19284 transcript(s): the cds cumulative length is
>   not a multiple of 3 for transcripts ‘ENST00000513161’
>   ‘ENST00000417833’ ‘ENST00000450884’ ‘ENST00000431193’
>   ‘ENST00000367667’ ‘ENST00000498306’ ‘ENST00000434641’
>   ‘ENST00000462097’ ‘ENST00000475119’ ‘ENST00000480643’
>   ‘ENST00000525843’ ‘ENST00000498419’ ‘ENST00000532678’
>   ‘ENST00000460428’ ‘ENST00000478853’ ‘ENST00000372925’
>   ‘ENST00000437607’ ‘ENST00000416121’ ‘ENST00000582567’
>   ‘ENST00000413489’ ‘ENST00000425265’ ‘ENST00000534717’
>   ‘ENST00000436685’ ‘ENST00000606954’ ‘ENST00000484054’
>   ‘ENST00000414971’ ‘ENST00000443667’ ‘ENST00000417191’
>   ‘ENST00000559578’ ‘ENST00000482110’ ‘ENST00000524607’
>   ‘ENST00000419169’ ‘ENST00000295713’ ‘ENST00000609181’
>   ‘ENST00000327794’ ‘ENST00000450490’ ‘ENST00000602582’
>   ‘ENST00000453676’ ‘ENST00000513088’ ‘ENST [... truncated]
> > txdb
> TranscriptDb object:
> | Db type: TranscriptDb
> | Supporting package: GenomicFeatures
> | Data source: UCSC
> | Genome: hg19
> | Organism: Homo sapiens
> | UCSC Table: ensGene
> | Resource URL: http://genome.ucsc.edu/
> | Type of Gene ID: Ensembl gene ID
> | Full dataset: yes
> | miRBase build ID: NA
> | transcript_nrow: 204940
> | exon_nrow: 584914
> | cds_nrow: 280379
> | Db created by: GenomicFeatures package from Bioconductor
> | Creation time: 2014-06-17 09:34:13 -0700 (Tue, 17 Jun 2014)
> | GenomicFeatures version at creation time: 1.16.2
> | RSQLite version at creation time: 0.11.4
> | DBSCHEMAVERSION: 1.0
>
> So you might try again. If you are on Windows, you might be having a proxy
> issue, in which case you might use the setInternet2() function prior to
> running makeTranscriptDbFromUCSC().
>
> Best,
>
> Jim
>
>
>
>
>
>>
>>
>> txdb <- makeTranscriptDbFromUCSC(genome='hg19',tablename='ensGene')
>>
>> Error in function (type, msg, asError = TRUE)  : couldn't connect to host
>>
>> I did install the required packages, so not what I am missing here.
>>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite()
>> biocLite(c("GenomicFeatures", "AnnotationDbi"))
>> library("GenomicFeatures")
>>
>> Could you please help me with this error.
>>
>> Many Thanks
>> Sharvari Gujja
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>
> _______________________________________________
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>

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