[BioC] GSEA GeneSetCollection

[Johnstone, Alice]

Hi
I have been using the GSEA java version to look at my microarray
results.  I ran into a problem as my samples are from rat.  I therefore
want to create my own gene sets based on KEGG and GO information in the
annotation packages.  I have used the command
gsc<-GeneSetCollection(Data,setType=KEGGCollection())
to create a collection, which is fine, but I want to be able to use this
with the java version.. is it possible to create/export a gmx or gmt
file from R from the GeneSetCollection object?
Thanks

Alice Johnstone

PhD Student
Institute of Environmental Science and Research Ltd
Kenepuru Science Centre
34 Kenepuru Drive
PO Box 50-348
Porirua
New Zealand

Tel:  + 64 4 914-0717
Fax: + 64 4 914-0770



> sessionInfo()
R version 2.7.0 (2008-04-22) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
Zealand.1252;LC_MONETARY=English_New
Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252

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

other attached packages:
 [1] GSEABase_1.2.1        multtest_1.20.0       simpleaffy_2.16.0
genefilter_1.20.0    
 [5] survival_2.34-1       sma_0.5.15            rat2302probe_2.2.0
rat2302cdf_2.2.0     
 [9] MASS_7.2-41           gcrma_2.12.1          matchprobes_1.12.0
illuminaRatBCv1_1.1.0
[13] beadarray_1.8.0       affy_1.18.0           preprocessCore_1.2.0
affyio_1.8.0         
[17] geneplotter_1.18.0    annotate_1.18.0       xtable_1.5-2
lattice_0.17-6       
[21] limma_2.14.1          pcot2_1.8.0           amap_0.8-2
rat2302.db_2.2.0     
[25] AnnotationDbi_1.2.0   RSQLite_0.6-8         DBI_0.2-4
Biobase_2.0.1        
[29] rat2302_2.2.0        

loaded via a namespace (and not attached):
[1] cluster_1.11.10    graph_1.18.0       grid_2.7.0
KernSmooth_2.22-22 RColorBrewer_1.0-2
[6] XML_1.93-2.1

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