[BioC] Error in .testGOFrame(x, organism) and invalid GO Evidence codes

Marc Carlson mcarlson at fhcrc.org
Tue Aug 6 00:38:24 CEST 2013

This error is complaining about a value for the middle column of the 
data.frame supplied to GOFrame.  I can't verify this though since I 
don't know which file from http://www.ebi.ac.uk/QuickGO/GAnnotation is 
the one you labeled as ppy_GOannot.txt (presumably GO terms for 
Orangutan), and the 1st 6 lines of your object all look basically OK.

Have you checked if any of the rows in your data.frame equal to the 
values that the error is complaining about?  Or could you maybe give me 
more specific directions to the file you are using?

Also, the third column of what you show could be a bit risky since those 
look like gene symbols.  And gene symbols are not good gene IDs.


On 08/05/2013 03:08 AM, Zhidong Yuan wrote:
> GOFrame(ppyGO,organism = "Pongo abelii")

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