Thanks Martin. I am using R3.0.0 on a PC.

John


________________________________
 From: Martin Morgan <mtmorgan@fhcrc.org>

@gene.com> 
Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> 
Sent: Thursday, November 21, 2013 2:40 PM
Subject: Re: [BioC] exon genomic coordinates


On 11/21/2013 02:21 PM, array chip wrote:
> Thank you Michael. I got an error message when running:
>
>> library(Homo.sapiens)
> Loading required package: GO.db
> Error : .onLoad failed in loadNamespace() for 'GO.db', details:
> Â  call: get(name, envir = asNamespace(pkg), inherits = FALSE)
> Â  error: object '.setDummyField' not found
> Error: package â€˜GO.dbâ€™ could not be loaded

I'm guess that you're using a mac and R-3.0.0

You'll need to either update your R to the current release R-3.0.2 or install 
the software needed to build R packages from source and update all of your
packages using type="source". It's easier to update your R, so I won't provide 
instructions for the latter.

The problem is that a backward incompatibility was introduced in the methods 
package going from R-3.0.0 to R-3.0.1. The incompatibility means that the 
Macintosh binaries we (Bioconductor) build with the current R only work with 
versions of R after the incompatiblity was introduced. So you either need to use 
a current R, or build the packages yourself.

Martin

>
>
> I already re-installing GO.db package, but still got the same error:
>
>> biocLite("GO.db")
> BioC_mirror: http://bioconductor.org
> Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.0.
> Installing package(s) 'GO.db'
> trying URL 'http://bioconductor.org/packages/2.12/data/annotation/bin/windows/contrib/3.0/GO.db_2.9.0.zip'
> Content type 'application/zip' length 25091062 bytes (23.9 Mb)
> opened URL
> downloaded 23.9 Mb
>
>
> John
>
>
> ________________________________
>   From: Michael Lawrence <lawrence.michael@gene.com>
>
> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
> Sent: Thursday, November 21, 2013 7:43 AM
> Subject: Re: [BioC] exon genomic coordinates
>
>
>
> Assuming human, use the Homo.sapiens package:
>
>
> library(Homo.sapiens)
> id <- select(Homo.sapiens, "KIT", "ENTREZID", "SYMBOL")$ENTREZID
> exons(Homo.sapiens, list(gene_id = id))
>
> It would be a lot nicer if exons() could take the gene symbol directly, but I've long given up trying to request that.
>
> The nice thing about this approach is that you have a GRanges, and you're not off in data.frame land.
>
>
>
>
>
>
>
>
> Hi,
>>
>>
>> Can anyone suggest how to retrieve the genomic coordinates for all exons for a given gene by say gene symbol? For example, how to retrieve the coordinates for all 21 exons for gene KIT?
>>
>> Thanks
>>
>> John
>> Â  Â  Â  Â  [[alternative HTML version deleted]]
>>
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>>
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>
>
>
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