[BioC] cateGOry error

[Seth Falcon]

Oleg Sklyar <osklyar at ebi.ac.uk> writes:

> Hi,
>
> I am having troubles with cateGOry as follows:
>
>  > m <- cateGOry(go$refseq_dna, go$go, FALSE)
> Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442 
> were mentioned in 'x' but were not found in the GO package.
>
> what this error means was not clear, so I tried those as indexes in my 
> data, as follows first, or as GO ids as follows second. Neither worked. 
> Any idea? Thanks, Oleg

What is typeof(go$go)?

Based on a quick read of the code in Cateogry/R/cateGOryMatrix.R, it
looks like these valus should be GO IDs (element of the categ argument
to cateGOry).  Are you sure those values are not in go$go?

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org