[BioC] ontoCompare (goTools) : goidvect error

[Robert Gentleman]

Hi Oana,
  Your R and bioconductor are still very out of date.  Unfortunately
there is no support
for such old versions, you really should be using the current release versions.

  best wishes
    Robert


On Wed, Aug 3, 2011 at 8:30 AM, Oana VIGY <oana.vigy at igf.cnrs.fr> wrote:
> Dear All,
>
> I'm using the "goTools" package in a script which is working fine for
> few years with the given system : R 2.5.1 and BioConductor 2.0.8.
>
> In 2009, I tried to upgrade BioConductor and R but I encountered
> time-consuming problems as others on the list (1st message by Scott
> Markel, 11/06/2009).
> So I keep the "old" versions.
>
> This time, I try again both upgrades as new versions of goTools have
> been released meantime but... I have the following errors :
>
> /Starting ontoCompare...
> Error in goidvect[test] : invalid subscript type 'list'/
>
> As input of the ontoCompare function is given a list of GO terms
> concerning the Molecular Function for the given test.
> Please find below the whole script and the sessionInfo.
>
> Thanks for any help.
>
> Best regards,
> Oana
>
>
> ##################
> ##### Script #######
>  > library(goTools)
> Loading required package: GO.db
> Loading required package: AnnotationDbi
> Loading required package: Biobase
>
> Welcome to Bioconductor
>
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
>
> Loading required package: DBI
>  > rankgo = as.numeric(2)
>  > root = "GO:0003674"
>  > listRank = CustomEndNodeList(root, rank=rankgo)
> rank= 1
> rank= 2
>  > pathData =
> paste("/var/www/html/tmp/YpFrh3eu/","AnnotationFile","MF",".txt",sep="");
>  > goAnnotation <- read.table(pathData, sep="\t", header=TRUE,
> colClasses="character")
>  > goAnnotation = as.vector(unlist(goAnnotation))
>  > Count = ontoCompare(list(goAnnotation), probeType="GO",
> method="TIDS", goType="MF")
> Starting ontoCompare...
> Error in goidvect[test] : invalid subscript type 'list'
>
> ###########
>  >sessionInfo()
> R version 2.10.0 (2009-10-26)
> x86_64-redhat-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
>
>
> ------------------------------------------------------------------------
> *Oana VIGY*
> Plate-forme de Protéomique Fonctionnelle (FPP)
> IGF, UMR 5203 CNRS - INSERM U661 - UM1 - UM2
> 141 rue de la Cardonille
> 34 094 Montpellier Cedex 5, France
> ------------------------------------------------------------------------
> Tel: +33 (0)4 34 35 92 39
> www.fpp.cnrs.fr <http://www.fpp.cnrs.fr>
> ------------------------------------------------------------------------
>
> --
> Passerelle antivirus IGF.
>
>
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>
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-- 
Robert Gentleman
rgentlem at gmail.com