[BioC] GOstats error messages

[Kimpel, Mark William]

I am getting error messages while using GOhyperG.

The first is when I try to pass along a list of LL identifiers that has duplicate entries. I get a message that says that the list must be unique. This is solved my using the unique() function. The vignette, however, seems to say that the function automatically takes into account the non-uniqueness of the identifiers. Is this just in relation to the annotation environment, not the user list?

The second is more serious and I don't know how to correct it. I am using the annotation package rat2302 and get "Error: value for 'M18349cds#1_s_at' not found". Using options recover I get: 


Enter a frame number, or 0 to exit   

1: GOHyperG.BP.MF.CC.func(x = unique(LL.vec[200:500]), annot.pckg)
2: GOHyperG(x, lib = annot.pckg, what = "BP")
3: sapply(goV, function(x) {
4: lapply(as.list(X), FUN, ...)
5: FUN(X[[1]], ...)
6: unique(unlist(mget(x, getDataEnv("LOCUSID", lib))))
7: unlist(mget(x, getDataEnv("LOCUSID", lib)))
8: mget(x, getDataEnv("LOCUSID", lib))
9: function (x) 

Selection: 9
Called from: eval(expr, envir, enclos)
Browse[1]> x
[1] "M18349cds#1_s_at"

It seems that the annotation package may have an error or something.

Am I doing something wrong? Is there a fix for this?

Thanks,

Mark


Mark W. Kimpel MD
 
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