[BioC] annotation information about ecoli2

[Marc Carlson]

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
>>
>>
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>