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

[Martin Morgan]

On 05/25/2012 06:13 AM, omranian wrote:
> 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 Hi Nooshin -- the AnnotationDbi package is slightly out of date with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?!

wait two days and try again; the package had a bug, the bug has been 
fixed (a few minutes ago); it takes a couple of days for the package to 
be checked and made available to you. When it is ready, using biocLite 
will download and install AnnotationDbi version 1.18.1. You must be 
using R version 2.15.0.

Martin

>
> Best,
> Nooshin


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