[BioC] RE : RE : RE : RE : maping SNPs

[Hervé Pagès]

On 01/12/2011 10:44 AM, Simon Noël wrote:
> Hi
>
> As you can see, the package GenomicRanges and IRanges  don't have the same version as yours on the supercomputer.  I will ask our informaticien to update them to the version you have and will see if now  makeTranscriptDbFromUCSC works.

Another option if you can't wait is that you make this TranscriptDb
object on another computer (where the BioC 2.7 installation is up
to date), save it to an SQLite file with saveFeatures(), move the
file to the supercomputer, and load it from there with loadFeatures().

Cheers,
H.


> I will let you know of any positive or negative result.
>
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-pc-linux-gnu (64-bit)
> locale:
>   [1] LC_CTYPE=en_CA.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_CA.UTF-8        LC_COLLATE=en_CA.UTF-8
>   [5] LC_MONETARY=C              LC_MESSAGES=en_CA.UTF-8
>   [7] LC_PAPER=en_CA.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>   attachedbase packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>   otherattached packages:
> [1] GenomicFeatures_1.2.3
> [2] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2
> [3] GenomicRanges_1.2.2
> [4] IRanges_1.8.7
>   loadedvia a namespace (and not attached):
>   [1] Biobase_2.10.0     biomaRt_2.6.0      Biostrings_2.18.2  BSgenome_1.18.2
>   [5] DBI_0.2-5          RCurl_1.5-0        RSQLite_0.9-4      rtracklayer_1.10.6
>   [9] tools_2.12.0       XML_3.2-0
>
>
> Simon Noël
> CdeC
> ________________________________________
> De : Hervé Pagès [hpages at fhcrc.org]
> Date d'envoi : 11 janvier 2011 21:05
> À : Simon Noël
> Cc : Valerie Obenchain; bioconductor at r-project.org
> Objet : Re: [BioC] RE : RE :  RE :  maping SNPs
>
>>      On     the    super    computer, it still doesn't work    and    on my
>>      computer, it still taking a lot of time.  What isn't working is
>>
>>      >   txdb<- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene")
>>       Downloadthe refGene table ... OK
>>       Downloadthe refLink table ... OK
>>       Extractthe 'transcripts' data frame ... OK
>>       Extractthe 'splicings' data frame ... OK
>>       Downloadand preprocess the 'chrominfo' data frame ... OK
>>       Preparethe 'metadata' data frame ... OK
>>       Makethe TranscriptDb object  ... Error  in  .writeMetadataTable(conn,
>>      metadata) : subscript out of bounds
>>      In addition: There were 50 or more warnings (use warnings() to see the first
>>      50)
>
>   Probablybecause some of the packages need to be updated on this machine
> (as you are already aware). See my sessionInfo below.
>
> Cheers,
> H.
>
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>    [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>    [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>    [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>    [7] LC_PAPER=en_US.utf8       LC_NAME=C
>    [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
>   attachedbase packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>   otherattached packages:
> [1] GenomicFeatures_1.2.3
> [2] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2
> [3] GenomicRanges_1.2.3
> [4] IRanges_1.8.8
>
>   loadedvia a namespace (and not attached):
> [1] Biobase_2.10.0     biomaRt_2.6.0      Biostrings_2.18.2
> BSgenome_1.18.2
> [5] DBI_0.2-5          RCurl_1.5-0        RSQLite_0.9-4
> rtracklayer_1.10.6
> [9] XML_3.2-0
>
>
>>
>>
>>      Simon Noël
>>      CdeC
>> _______________________________________________
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>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M2-B876
>   P.O.Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

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