[BioC] Odd isolated problem with GOstats

[Marc Carlson]

Marc Carlson wrote:
> Mark W Kimpel wrote:
>   
>> I have used a custom wrapper function to invoke GOstats for almost a 
>> year without problem. Now, with just one dataset, I am getting an error. 
>> Not sure if this is a bug or something very odd about just my one 
>> dataset. The GO:ID that yields the error is a valid ID, I checked. I am 
>> using the devel version and rechecked after just updating my packages.
>>
>> Any ideas as to what the problem might be?
>>
>> Loading required package: rat2302
>> Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
>>    invalid key "GO:0016089"
>>
>> Enter a frame number, or 0 to exit
>>
>>   1: limma.contrast.output.func(AOP, fit2, rslt, contrast.num = 1, 
>> custom.contra
>>   2: GO.anal.func(input.df = t.tab.annot.obj$sig.named.genes, 
>> annotationPckg = a
>>   3: GOHyperMaxCats.func(optimizedParam)
>>   4: data.frame(summary(test.obj))
>>   5: summary(test.obj)
>>   6: summary(test.obj)
>>   7: .local(object, ...)
>>   8: sapply(mget(goIds, GOenv("TERM")), Term)
>>   9: lapply(X, FUN, ...)
>> 10: is.vector(X)
>> 11: mget(goIds, GOenv("TERM"))
>> 12: mget(goIds, GOenv("TERM"))
>> 13: `keys<-`(`*tmp*`, value = c("GO:0007268", "GO:0007214", 
>> "GO:0050877", "GO:0
>> 14: `keys<-`(`*tmp*`, value = c("GO:0007268", "GO:0007214", 
>> "GO:0050877", "GO:0
>> 15: switch(as.character(direction(x)), "1" = `Lkeys<-`(x, value), "-1" = 
>> `Rkeys
>> 16: `Lkeys<-`(x, value)
>> 17: `Lkeys<-`(x, value)
>> 18: .checkKeys(value, Lkeys(x), x at ifnotfound)
>>
>>
>>  > sessionInfo()
>> R version 2.7.0 Under development (unstable) (2007-12-20 r43739)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] splines   tools     stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>>   [1] rat2302_2.0.1        affycoretools_1.11.2 annaffy_1.11.1
>>   [4] KEGG_2.0.1           GO_2.0.1             gcrma_2.11.1
>>   [7] matchprobes_1.11.0   biomaRt_1.13.6       RCurl_0.8-3
>> [10] GOstats_2.5.0        Category_2.5.0       genefilter_1.17.7
>> [13] survival_2.34        RBGL_1.15.7          annotate_1.17.3
>> [16] xtable_1.5-2         GO.db_2.1.1          AnnotationDbi_1.1.8
>> [19] RSQLite_0.6-4        DBI_0.2-4            graph_1.17.14
>> [22] limma_2.13.3         affy_1.17.3          preprocessCore_1.1.5
>> [25] affyio_1.7.9         Biobase_1.17.8
>>
>> loaded via a namespace (and not attached):
>> [1] cluster_1.11.9 XML_1.93-2
>>   
>>     

If you could show me what it is that your script is doing (some source
code) then I might be better able to help you with this.  But as it
stands right now I have very few specifics about what you are trying to
do.  I can see you posted the sessionInfo() which helps me know what
versions of things you are using.  But what is this script that you
speak of?  What does that code  actually look like?  I am afraid that I
don't have a patch for you because the annotation package is not
actually broken, and is only missing information because of what was
available at GO at the precise moment when that package was made.  I
can't tell you why GO decided to remove that particular term and then
later on decided to add it back in, but  I looked at data that we
gathered from them to build annotations at different time points and
that is what has actually happened in this case.

>From your previous posts, it looks like your trouble is caused because
you are missing a key and then looking for that missing key in an
environment.  If that is what is happening, then I think you should code
things in a way so that you can filter out keys that are not present.

More specifically I think that you probably just want to do some minor
cleanup before you call something like mget() to make sure that your
keys are actually present.  Here is a quick example of how this might look:

library(GO.db)

myKeys = c("FAKEID","GO:0000006","GO:0000003")

myKeys[myKeys %in% keys(GOTERM)]


Hope this helps,


     Marc