Hi Hotz:

    Many thanks for the link. I found the file I need from it.

Best regards,
Wei

Hotz, Hans-Rudolf wrote:
>
> On 3/17/09 6:58 AM, "Wei Shi" <shi@wehi.edu.au> wrote:
>
>   
>> Dear list,
>>
>>    The annotation package "org.Mm.eg.db" provides UCSC's annotation for
>> mouse genes. However, this annotation could sometime be different from
>> NCBI's annotation. Below is an example:
>>
>> library(org.Mm.eg.db)
>> mget("Tff1", org.Mm.egSYMBOL2EG)
>> $Tff1
>> [1] "21784"
>> mget("21784", org.Mm.egCHRLOC)
>> $`21784`
>>         17          5
>>  -31298340 -143285576
>>
>>     Two chromosomal locations were found for "Tff1" which are on
>> chromosome 17 and chromosome 5 respectively. However, this genes is only
>> located on chromosome 17 according to NCBI Entrez gene database. Does
>> anybody know if there is any packages or other sources which provide
>> NCBI gene annotation? I am working on a large set of genes and NCBI does
>> not seem to provide downloadable files which contain gene information
>> such as chromosomal locations etc.
>>     
>
> The files on "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/" should contain all the
> data you want. 
>
>
> Regards, Hans
>
>   
>>> sessionInfo()
>>>       
>> R version 2.8.1 (2008-12-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=
>> English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>>
>> attached base packages:
>> [1] tools     stats     graphics  grDevices utils     datasets
>> methods   base   
>>
>> other attached packages:
>> [1] org.Mm.eg.db_2.2.6  RSQLite_0.7-1       DBI_0.2-4
>> AnnotationDbi_1.4.3 Biobase_2.2.2
>>
>>
>> Thanks,
>> Wei
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>     
>
>   

	[[alternative HTML version deleted]]

