[BioC] annotation information about ecoli2

[James W. MacDonald]

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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> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662