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

[Martin Morgan]

On 05/25/2012 06:33 AM, omranian wrote:
> 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 Hi Nooshin -- the AnnotationDbi package is slightly out of date with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
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>>>
>>> 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.

biocLite should not be installing AnnotationDbi 1.14.1 when using R 
2.15. If that is really the case, then please report (copy and paste) 
the result of running the following commands in a new R session.

   source("http://bioconductor.org/biocLite.R")
   biocLite("AnnotationDbi")
   sessionInfo()

Martin

>
> Best,
> Nooshin


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793