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

[omranian]

On 05/25/2012 03:20 PM, Martin Morgan wrote:
> 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 Hi Nooshin -- the AnnotationDbi package is slightly out of date with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
>
>
Thanks a lot.
So, you believe if I wait it would work!
I have R version 2.15.0 but the version of AnnotationDbi is 1.14.1 even 
when I uninstall and install it again.
So I'll wait for two days and try it again.
I hope it works by then.

Best,
Nooshin