[BioC] GOstats error messages

Robert Gentleman rgentlem at fhcrc.org
Mon Sep 19 20:19:57 CEST 2005


  The posting guide does ask you to provide the output of sessionInfo, 
as well as examples that can be cut and pasted.

Kimpel, Mark William wrote:
> 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 manual page is unequivocal:

says (among other things)


      GOHyperG(x, lib="hgu95av2", what="MF")


        x: A vector of unique LocusLink identifiers.

  Manual pages are where you should look for this sort of information.

If you give a specific set of line numbers for the part of the vignette 
that seems to be in error, I will fix it to align with the manual page.

  Best wishes,

ps the second questions seems to have already been addressed
> 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
> Official Business Address:
> Department of Psychiatry
> Indiana University School of Medicine
> Biotechnology, Research, & Training Center
> 1345 W. 16th Street
> Indianapolis, IN  46202
> Preferred Mailing Address:
> 15032 Hunter Court
> Westfield, IN  46074
> (317) 490-5129 Home, Work, & Mobile
> 1-(317)-536-2730 FAX
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor

Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

More information about the Bioconductor mailing list