[BioC] Odd isolated problem with GOstats

Mark W Kimpel mwkimpel at gmail.com
Thu Jan 3 21:35:48 CET 2008

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, 
  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" = 
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)


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

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

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(317) 204-4202 Home (no voice mail please)


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