Hi, thanks for your help.

The information I need is the 'rn4' coordinates of Entrez Genes,  so I
finally used the 'refGene' table and 'refLink' table downloaded from UCSC
genome browser database under the directory of 'rn4', and got what I need.
As for other information not related to the chromosomal locations, I just
used the information in the package  'org.Rn.eg.db'.

Maybe the maintainner can still provide official packages based on 'rn4',
say, 'org.Rn4.eg.db', since annotation based on 'rn5' is not as complete as
that based on 'rn4'.

Best,
ZQ

On Sat, Dec 21, 2013 at 8:53 AM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Steve is right.  You could go and do that.  However in this case we have
> already done the work for you.  You can find a package here:
>
> http://www.bioconductor.org/packages/release/data/annotation/html/TxDb.
> Rnorvegicus.UCSC.rn4.ensGene.html
>
> That should get you transcript locations for RN4.
>
> For more information about how you can make use of that resource and of
> others like it, please be sure to also peak at our workflow:
>
> http://www.bioconductor.org/help/workflows/annotation/annotation/
>
>
>   Marc
>
>
>
>
>
> On 12/18/2013 10:09 PM, Steve Lianoglou wrote:
>
>> Hi,
>>
>> On Wed, Dec 18, 2013 at 6:20 PM, Zhi-Qiang Ye <yezhiqiang@gmail.com>
>> wrote:
>>
>>> Hi, all
>>>
>>>          I need to analysis genes whose chromosomal locations are based
>>> on
>>> the rat genome version rn4, so installed 'org.Rn.eg.db'. However, the
>>> genome coordinate system is based on rn5.
>>>
>>>           Is there any way to get and install old versions of
>>> 'org.Rn.eg.db'?
>>>
>> You might consider building a TranscriptDb object from rn4 annotations
>> using the GenomicFeatures package:
>>
>> http://bioconductor.org/packages/release/bioc/html/GenomicFeatures.html
>>
>> Read through its vignette to figure out how to download and build a
>> TranscriptDb from UCSC. It's going to be something like:
>>
>> R> library(GenomicFeatures)
>> R> txdb <- makeTranscriptDbFromUCSC(genome='rn4', tablename='ensGene')
>>
>> Keep reading to figure out how to lookup genes/transcripts by
>> (ensembl) transcript IDs, and I think you should be good to go.
>>
>> If you need to do sequence related analyses using these annotations,
>> you can use the rn4 BSgenome object, to boot:
>>
>> http://bioconductor.org/packages/release/data/annotation/html/BSgenome.
>> Rnorvegicus.UCSC.rn4.html
>>
>> HTH,
>> -steve
>>
>>
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