[BioC] goTools: Error in goidvect[test] : invalid subscript type \'list\'

[Brad Davis [guest]]

I am having some difficulty with the goTools package.  Specifically I am getting the error message Error in goidvect[test] : invalid subscript type 'list'

First I load the GOTerms

goAnnotation2 <- read.table("C:/Users/Kristi 2/Desktop/test.txt", sep="\t", header=TRUE, colClasses="character")

Which looks like this

GOTerm
GO:0050517
GO:0050432
GO:0005515
GO:0003677
GO:0008270
GO:0030548
GO:0050517
GO:0050432
GO:0005515
GO:0051010

goAnnotation2 <- as.vector(unlist(goAnnotation2))
class(goAnnotation2)
[1] "character"

Count = ontoCompare(list(goAnnotation2), probeType="GO", method="TIDS")
Starting ontoCompare...
Error in goidvect[test] : invalid subscript type 'list'

I found a similar error discussed August 4, 2011.  The OP posted the code that they could not execute successfully on their machine, although the example they gave worked for me.  

I'm running Windows 7 box, core i7 processor with 8GB RAM, and I'm using R-Studio.

Note, that the above list of GO terms isn't the actual list of GO terms I wish to include, it's just a random I am starting with to get my hands wet with goTools.  I have some work to do yet to extract all the GO terms from our microarray annotation file which annoyingly included the textual descriptions for each GO term beside it (e.g. GO:0032422: purinE-rich negative regulatory element binding; GO:0003714: transcription corepressor activity; GO:0003700: transcription factor activity)

Thanks,
Brad



 -- output of sessionInfo(): 

R version 2.14.1 (2011-12-22)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252    LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C                    LC_TIME=English_Canada.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] goTools_1.28.0        GO.db_2.6.1           RSQLite_0.11.1        DBI_0.2-5            
[5] AnnotationDbi_1.16.19 Biobase_2.14.0       

loaded via a namespace (and not attached):
[1] IRanges_1.12.6 tools_2.14.1  

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