It seems like the problem I was having may be related to specific GO ids
rather than anything else.  Instead of manually creating a sample list of
GO codes, I completed my code for automatically extracting the GO codes
from the provided annotations.  It more or less works if exclude
problematic GO ids as identified using options(error=recover).  e.g.  The
ontoCompare function fails and returns an error of

1: ontoCompare(list(alist[[1]][c(1:100)]), probeType="GO", methods="TIDS",
goType="BP", plot=TRUE)
2: lapply(tmp, parentsVectWrapper, endnode)
3: FUN(X[[2]])

Suggests that it's element 2 from alist (e.g. alist[[2]]), which in this
case is GO:0000022.

Once I remove that element from the list, ontoCompare proceeds past that
point and either executes successfully if I submit a short enough list
(e.g. alist[[1]][c(1,3:50)]) or until it highlights another problematic
element.  Oddly, in some situations when this happens, the error will
identify position n as being problematic and then when I remove it, it will
identify position n-1 as being problematic, and so on and so forth.

I've tried randomizing the index from the GO list (i.e. swapping the GO ids
between index 21 and 43, for example) to determine if it's in anyway
related to run time or loop time, but that doesn't seem to be the case.

In any event, here are a sample of the GO ids that seem to be causing me
problems.  I do not see any obvious pattern here.

GO:0000910, GO:0043193, GO:006468, GO:0007243, GO:0045449, GO:0007015

Brad

On Fri, Jul 6, 2012 at 12:14 PM, James W. MacDonald <jmacdon@uw.edu> wrote:

> Hi Brad,
>
>
> On 7/6/2012 2:55 PM, Brad Davis [guest] wrote:
>
>> 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 believe you need a list of length > 1. I can't get your code to run
> either, but this works:
>
> > gos <- Lkeys(GOTERM)
> > golst <- list(gos[sample(1:1000, 20)], gos[sample(1:1000,
> 20)],gos[sample(1:1000, 20)])
> > z <- ontoCompare(golst, probeType="GO", method="TIDS")
>
> Best,
>
> Jim
>
>
>
>
>> 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
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

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