[BioC] annotation information about ecoli2

[Marc Carlson]

Hi Jim,

There is an updated list of supported species in inst/NEWS file for the
AnnotationDbi package.  You can also just look for appropriate ".db0"
files on offer at the web site the way that you could search for a
platform specific package.  Only the intermediate databases end with the
".db0" extension.

http://www.bioconductor.org/packages/release/data/annotation/


  Marc



James W. MacDonald wrote:
> Thanks, Marc. I know you recently posted on the listserv which species
> have a .db0 file (and for which a annotation package can be built),
> but is there somewhere that an updated list is posted of the available
> species?
>
> Best,
>
> Jim
>
>
>
> Marc Carlson wrote:
>> Hi guys,
>>
>> You could make a package using the SQLForge code in the AnnotationDbi
>> package.  Here is where you can find a vignette to explain how to use
>> it:
>>
>> http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html
>>
>>  
>>   Marc
>>
>>
>> James W. MacDonald wrote:
>>> Hi Minwook,
>>>
>>> Minwook Kim wrote:
>>>> Hi,
>>>> I run the aafTableAnn() to get the annotation information of eocli2.
>>>> But I got the error. I did try to get the ecoli package. but it
>>>> failed. Anyone help me?
>>>>> AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]);
>>>> Loading required package: ecoli2
>>>> Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2
>>>> In addition: Warning message:
>>>> In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>> logical.return = TRUE,  :
>>>>   there is no package called 'ecoli2'
>>> This is true. In addition, there is no ecoli2.db package, nor can I
>>> find any Biomart servers that might help. So for the time being, it
>>> appears the best bet for annotation is the annotation file from
>>> Affymetrix.
>>>
>>> http://www.affymetrix.com/Auth/analysis/downloads/na26/ivt/E_coli_2.na26.annot.csv.zip
>>>
>>>
>>>
>>> You can make HTML or text tables using this file and the annotate
>>> package if that is what you are trying to do - see the 'Get HTML
>>> Output' vignette.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>>
>>>>
>>>> Apparently, the following information are helpful to fix it.
>>>>> chiptype
>>>> [1] "ecoli2"
>>>>  
>>>> "AllGenes" variable includes probe ids.
>>>>
>>>> I guess "ecoli2" microarry is not supported by annaffy package. or I
>>>> don"t know how to download the ecoli2 package.
>>>> Thanks.
>>>> Minwook
>>>>
>>>>
>>>>>  sessionInfo()
>>>> R version 2.7.0 (2008-04-22) x86_64-redhat-linux-gnu locale:
>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>>>
>>>>
>>>> attached base packages:
>>>> [1] splines   tools     stats     graphics  grDevices utils   
>>>> datasets [8] methods   base     other attached packages:
>>>>  [1] gplots_2.6.0         gdata_2.4.2          gtools_2.5.0      
>>>>  [4] simpleaffy_2.16.1    ecoli2probe_2.2.0    ecoli2cdf_2.2.0   
>>>>  [7] bioDist_1.12.0       genefilter_1.20.1    survival_2.34-1   
>>>> [10] annaffy_1.12.1       KEGG.db_2.2.0        GO.db_2.2.0       
>>>> [13] AnnotationDbi_1.2.2  RSQLite_0.7-1        DBI_0.2-4         
>>>> [16] gcrma_2.12.1         matchprobes_1.12.1   affy_1.18.2       
>>>> [19] preprocessCore_1.2.1 affyio_1.8.1         Biobase_2.0.1     
>>>> loaded via a namespace (and not attached):
>>>> [1] annotate_1.18.0
>>>>
>>>>
>>>>
>>>>
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>>
>