[BioC] Error in .testGOFrame(x, organism)

[omranian]

On 05/25/2012 03:09 PM, Martin Morgan wrote:
> On 05/25/2012 02:35 AM, omranian wrote:
>> Hello,
>>
>> Can anybody help me to solve this error? I can not understand it :(
>>
>> library(org.Sc.sgd.db)
>> frame <- toTable(org.Sc.sgdGO)
>> goframeData <- data.frame(frame$go_id, frame$Evidence,
>> frame$systematic_name)
>> goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae")
>> Loading required package: GO.db
>>
>> Error in .testGOFrame(x, organism) :
>> All of the Evidence codes in your data.frame object must be legitimate
>> Evidence Codes.
>
> Hi Nooshin -- the AnnotationDbi package is slightly out of date with 
> respect to Evidence codes it selects; this is fixed in AnnotationDbi 
> 1.18.1, which will be available for download via biocLite in a day or 
> so. A work-around is to drop the 13 'IRD' evidence codes,
>
> > idx = goframeData$frame.Evidence != "IRD"
> > table(idx)
> idx
> FALSE  TRUE
>    13 73735
> > goframeData = goframeData[idx,]
>
> Martin
>
>>
>> Thanks a lot.
>> Nooshin
>>
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>
>
Hi Martin,
Thanks for the reply!
I removed the package and reinstalled it many times, but doesn't help :(

I used biocLite to install and hope it installed the latest version.
Now, I really don't know what should I do?!

Best,
Nooshin