[BioC] annotation information about ecoli2

[James W. MacDonald]

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