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

[Martin Morgan]

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Hi Nooshin -- the AnnotationDbi package is slightly out of date with 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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