[BioC] GSEA GeneSetCollection

[Johnstone, Alice]

Thanks Martin!
The code worked and there were no problems importing the file.
Regards 
Alice


-----Original Message-----
From: Martin Morgan [mailto:mtmorgan at fhcrc.org] 
Sent: Saturday, 7 June 2008 1:54 a.m.
To: Johnstone, Alice
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] GSEA GeneSetCollection

Hi Alice --

"Johnstone, Alice" <Alice.Johnstone at esr.cri.nz> writes:

> 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?

I don't think there's functionality available, but the following will
create a gmt file, I think (untested beyond file creation)

makeRow <- function(set)
    paste(setName(set), description(set),
          paste(geneIds(set), collapse="\t"),
          sep="\t")
writeLines(sapply(gsc, makeRow), "/tmp/rats.gmt")

Martin

> 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
>
> P Think before you print
> This e-mail transmission and any attachments that accompany it may
contain information that is privileged, confidential or otherwise exempt
from disclosure under applicable law and is intended solely for the use
of the individual(s) to whom it was intended to be addressed.
> If you have received this e-mail by mistake, or you are not the
intended recipient, any disclosure, dissemination, distribution, copying
or other use or retention of this communication or its substance is
prohibited. If you have received this communication in error, please
immediately reply to the author via e-mail that you received this
message by mistake and also permanently delete the original and all
copies of this e-mail and any attachments from your computer. Thank you.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: 
> http://news.gmane.org/gmane.science.biology.informatics.conductor

--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center 1100
Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793