Thank you Adrian, following the instructions, I got it to work!

Another question, can you provide a rough calculation of the memory usage
of a topGOdata object, given the number of GO terms and genes?

Thanks,
-JJ

-- 
JJ Chai
National Center for Computational Sciences
Computer Science and Mathematics Div
Oak Ridge National Laboratory


On Thu, Jan 16, 2014 at 11:41 AM, Adrian Alexa <adrian.alexa@gmail.com>wrote:

> Hi JJ,
>
> yes, you should be able to do that with topGO. Please read through Section
> 4.3 in the package vignette on how to use custom annotations:
>
> http://www.bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf
>
> You can't specify a level and chose to test only the GO terms on that
> level. That won't be much useful and it won't really take advantage of the
> GO hierarchy.
>
> Hope this helps.
>
>
> Regards,
> Adrian Alexa
>
>
>
>
>
> On Wed, Jan 15, 2014 at 10:40 PM, JJ [guest] <guest@bioconductor.org>wrote:
>
>>
>> I have annotated some genomes with my own protein function annotation
>> pipeline. Each genome will have a list of genes and their corresponding GO
>> terms. In my annotation, the GO terms are on all kinds of different levels
>> because of the hierarchical structure of GO itself.
>>
>> So my input will be all the GO terms for one (or a few) genome of
>> interest, and a bigger set of background GO terms. I would like to figure
>> out which GO terms are enriched in the interesting genomes and what they do.
>>
>> It'll be great if I could also specify on what level the GO terms are
>> summarized.
>>
>> Can topGO handle this kind of problem? If not, any suggestions?
>>
>> Thanks a lot!
>>
>> -JJ
>>
>>
>>
>>
>>
>>  -- output of sessionInfo():
>>
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] grid      parallel  stats     graphics  grDevices utils     datasets
>>  methods   base
>>
>> other attached packages:
>>  [1] AnnotationForge_1.4.4 org.Hs.eg.db_2.10.1   GOFunction_1.10.0
>> Rgraphviz_2.6.0
>>  [5] ALL_1.4.16            topGO_2.14.0          SparseM_1.03
>>  GO.db_2.10.1
>>  [9] RSQLite_0.11.4        DBI_0.2-7             AnnotationDbi_1.24.0
>>  Biobase_2.22.0
>> [13] BiocGenerics_0.8.0    graph_1.40.1          BiocInstaller_1.12.0
>>
>> loaded via a namespace (and not attached):
>> [1] IRanges_1.20.6  lattice_0.20-24 stats4_3.0.2    tools_3.0.2
>>
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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>
>

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