[BioC] cateGOry error

[Wolfgang Huber]

Dear Oleg,

please use a more recent version of cateGOry, where I have fixed the 
error message to be more meaningful. It means that you are supplying GO 
categories for which there is no information in the Bioconductor GO 
package, either because they have been retired or because they have been 
created after the package was made.

See also:
https://stat.ethz.ch/pipermail/bioc-devel/2007-May/001108.html


Regarding your NA problem, as Jim already pointed out, isn't this 
equivalent to

  a="gaga"
  a[2]
[1] NA

  Best wishes
  Wolfgang


  Sklyar ha scritto:
> 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
> 
>  > index <- c(24, 172, 1978, 1979, 4441)
>  > m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE)
> Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442 
> were mentioned in 'x' but were not found in the GO package.
> 
>  > terms <- c("GO:0000024", "GO:0000172", "GO:0001978", "GO:0001979", 
> "GO:0004442")
>  > index <- which(go$go %in% terms)
>  > go$go[index]
> [1] "GO:0000172" "GO:0000172"
> 
>  > m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE)
> Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4441 
> were mentioned in 'x' but were not found in the GO package.
> 


-- 

Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber