Hi Brad,

thanks for your explanations and advices.
It's meaningful.

Best regards,
Oana

Le 08/08/2012 20:00, Brad Davis a écrit :
> Hi Oana,
>
> I suspect the problem is actually with GO.db rather than goTools.  The 
> problems I ran in to involved GO terms that were either deprecated or 
> where alternate IDs for the main GO ID.  My workaround for this was to 
> take my list of GO ids and compare it to the list of deprecated GO 
> terms , removing any that match- then as the program would run, I'd 
> keep a manual list of GO ids that didn't work because of the alternate 
> id problem, and I had a little script I wrote to pre-emptively find 
> and change those to the main GO ids which did work.
>
> Brad
>
>
> On Wed, Aug 8, 2012 at 4:41 AM, Oana VIGY <oana.vigy@igf.cnrs.fr 
> <mailto:oana.vigy@igf.cnrs.fr>> wrote:
>
>     Dear Agnes,
>
>     I encountered a similar issue last summer (see related messages on
>     the list - August 2011) and exchanged few emails directly with
>     Jean about that (+copy to you).
>
>     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 (goTools 1.8) and I try several times to upgrade R & Co. but
>     I faced then the kind of problem which was reported by Brad and
>     time-consuming problems.
>
>     It's quite difficult to maintain an old system and perhaps it is a
>     non-sense to continue performing analysis with the old package.
>
>     Please let us know how it goes.
>
>     Best regards,
>
>     Oana
>
>
>     Le 12/07/2012 22:01, Agnes Paquet a écrit :
>>     Hi Brad,
>>
>>     I will take a look and see if there is an easy fix. Sorry for the trouble you are having using the package.
>>
>>     Agnes
>>
>>     On Jul 12, 2012, at 12:29 PM, Brad Davis [guest]<guest@bioconductor.org>  <mailto:guest@bioconductor.org>  wrote:
>>
>>>     Hello everyone,
>>>
>>>     I am having some difficulty with ontoCompare when providing it with a list of GO terms.  Here is an example of the output that I get when the function fails:
>>>
>>>
>>>>     ontoTest <- ontoCompare(list(gotermslist), probeType="GO", goType="BP", plot=TRUE)
>>>     Starting ontoCompare...
>>>     Error in goidvect[test] : invalid subscript type 'list'
>>>
>>>     Enter a frame number, or 0 to exit
>>>
>>>     1: ontoCompare(list(gotermslist), probeType = "GO", goType = "BP", plot = TRUE)
>>>     2: lapply(tmp, parentsVectWraper, endnode)
>>>     3: FUN(X[[2554]], ...)
>>>
>>>>     gotermslist[2554]
>>>     [1] "GO:0051605"
>>>
>>>     Using Amigo to look up this GO term shows this GO ID is an alternate ID to GO:0016485, but using the Synonym function from GO.db on GO:0051605 doesn't provide any useful information.
>>>
>>>
>>>>     Synonym("GO:0051605")
>>>     $<NA>
>>>     NULL
>>>
>>>     Conversely, running Synonym on GO:0016485 identifies GO:0051605 as a valid alternate id
>>>
>>>
>>>>     Synonym("GO:0016485")
>>>     $`GO:0016485`
>>>     [1] "peptidolysis during protein maturation"
>>>     [2] "protein maturation by peptide bond cleavage"
>>>     [3] "protein maturation by peptide bond hydrolysis"
>>>     [4] "protein maturation by proteolysis"
>>>     [5] "GO:0051605"
>>>
>>>     I run into the same problem with GO:0006345, which is an alternate ID for GO:0031936 (which doesn't cause a problem for ontoCompare).
>>>
>>>     It seems like this represents some sort of mapping problem with GO.db, but I don't know how to address it myself.  Any suggestions?
>>>
>>>     In other cases, ontoCompare fails when there doesn't seem to be any problem with the GO id, at least so far as I can tell, e.g. GO:0055086. Amigo doesn't show any alternate ids nor does it indicate that the term is obsolete, so I don't understand why it's not working- but it is very frustrating.
>>>
>>>     I would appreciate any suggestions.
>>>
>>>
>>>
>>>
>>>
>>>
>>>     -- output of sessionInfo():
>>>
>>>>     sessionInfo()
>>>     R version 2.15.1 (2012-06-22)
>>>     Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>>     locale:
>>>     [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
>>>     [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
>>>     [5] LC_TIME=English_Canada.1252
>>>
>>>     attached base packages:
>>>     [1] compiler  grid      stats     graphics  grDevices utils     datasets  methods   base
>>>
>>>     other attached packages:
>>>     [1] Vennerable_2.2        xtable_1.7-0          reshape_0.8.4         plyr_1.7.1
>>>     [5] RColorBrewer_1.0-5    lattice_0.20-6        RBGL_1.30.1           graph_1.32.0
>>>     [9] manipulate_0.96.316   annotate_1.32.3       goTools_1.28.0        GO.db_2.6.1
>>>     [13] RSQLite_0.11.1        DBI_0.2-5             AnnotationDbi_1.16.19 Biobase_2.14.0
>>>     [17] nlme_3.1-104          car_2.0-12            nnet_7.3-4            gplots_2.11.0
>>>     [21] MASS_7.3-19           KernSmooth_2.23-8     caTools_1.13          bitops_1.0-4.1
>>>     [25] gdata_2.11.0          gtools_2.7.0
>>>
>>>     loaded via a namespace (and not attached):
>>>     [1] IRanges_1.12.6 tools_2.15.1
>>>
>>>     --
>>>     Sent via the guest posting facility atbioconductor.org  <http://bioconductor.org>.
>>     _______________________________________________
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>>
>
>     -- 
>     *Oana VIGY*
>
>     *! Changement d'adresse email : oana.vigy@fpp.cnrs.fr
>     <mailto:oana.vigy@fpp.cnrs.fr> !*
>
>     Plate-forme de Protéomique Fonctionnelle (FPP)
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>
>
>
>
>     -- 
>     Passerelle antivirus IGF
>
>
>
> -- 
> Passerelle antivirus IGF 

-- 
*Oana VIGY*

*! Changement d'adresse email : oana.vigy@fpp.cnrs.fr !*

Plate-forme de Protéomique Fonctionnelle (FPP)
c/o 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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