[BioC] get.annotation problem with vitis vinifera

[Saroj Mohapatra]

Hi Tarun:

I think you need an annotation package in addition to the cdf package. 
Perhaps the annotation package for Vitis vinifera does not yet exist 
(but I am not sure).

In addition, perhaps the command

annot <- get.annotation(x, "vitisviniferacdf")

should be replaced by

annot <- get.annotation(x, "vitisvinifera") ?

I tried the following:

----
library(hgu95aprobe)
library(hgu95acdf)
library(simpleaffy)

hgu95aprobe[1,4]
[1] "1000_at"

get.annotation(hgu95aprobe[1,4], "hgu95a")
    gene name
[1,] "MAPK3"
    
accession                                                                  
[1,] 
"=HYPERLINK(\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=nucleotide&term=X60188\",\"X60188\")" 

    
unigene                                                                    
[1,] 
"=HYPERLINK(\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=unigene&term=Hs.861&dopt=unigene\",\"Hs.861\")" 

    description
[1,] "mitogen-activated protein kinase 3"


library(vitisviniferaprobe)
library(vitisviniferacdf)

vitisviniferaprobe[1,4]
[1] "1606449_at"

get.annotation(vitisviniferaprobe[1,4], "vitisvinifera")
Error in library(cdfname, character.only = T) :
       there is no package called 'vitisvinifera'

----

Best,

Saroj

Tarun Nayar wrote:
> Hi,
>  
> I'm trying to get annotations for the grape chip; Vitis Vinifera, using
> the simpleaffy command get.annotation. The cdfName function returns the
> wrong cdfname (VitisVinifera); when I enter the 'real' cdfname
> (vitisviniferacdf), I get another error.
>  
>   
>> cdfName(raw.data)
>>     
> [1] "Vitis_Vinifera"
>   
>> annot <- get.annotation(x, "Vitis_Vinifera")
>>     
> Error in library(cdfname, character.only = T) : 
>         there is no package called 'Vitis', version Vinifera
>
>   
>> annot <- get.annotation(x, "vitisviniferacdf")
>>     
> Error in get(x, envir, mode, inherits) : variable
> "vitisviniferacdfSYMBOL" was not found
>
> Any ideas?
>  
> Tarun Nayar
> Genome Sciences Centre
> Vancouver, BC
>
> 	[[alternative HTML version deleted]]
>
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