[BioC] How can I make genesets for sigpathway

[Srinivas Iyyer]

Dear Jim , 
thanks for your input. 
 For now I am using U133Plus2 and Later I will be
using affy and agilent mouse and rat chips
respectively. 

Although, I found the site where they are describing
how to make "G" object, the script that was provided
is not straightforward and I get errors when I am
trying to process what the author is asking me to do.(
http://www.chip.org/~ppark/Supplements/PNAS05.html)


My ultimate aim is to combine my choice of datasets:
some from MsigDB, my own annotations, PPI sets etc.
into "G"list object. 

For that the starting material I have is a TAB delim
file with:

Pathway Source    Name of Pathway   GENE symbols. 


Now I am clueless as how to create a annotation list.
This is required to start doing what authors are
describing in their code how to convert gene symbols
to ID. 

Simply, I dont know how to make an object equivalent
to "Genesets_EntrezGeneIDs.RData". 

"Genesets_EntrezGeneIDs.RData" is an R workspace
containing Entrez GeneIDs corresponding to gene sets
from GO, KEGG, and other pathway databases. 





egidDir <- getwd()
> egidDir
[1] "C:/Documents and Settings/srini/My
Documents/software"

>load(file.path(egidDir,
"Genesets_EntrezGeneIDs.RData"))
> biocAnnot <- "rat2302"
> library(biocAnnot, character.only = TRUE)
Error in library(biocAnnot, character.only = TRUE) : 
  there is no package called 'rat2302'
> biocAnnot
[1] "rat2302"
> ls()
[1] "biocAnnot" "egidDir"   "G.EGIDs"  
> xx <- as.list(get(paste(biocAnnot, "ENTREZID", sep =
"")))
Error in get(paste(biocAnnot, "ENTREZID", sep = "")) :

> sessionInfo()
R version 2.6.1 (2007-11-26) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United
States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United
States.1252

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

other attached packages:
[1] sigPathway_1.6.0

loaded via a namespace (and not attached):
[1] rcompgen_0.1-17 tools_2.6.1    


This might be as simple stupid question as how to make
lists in R. But truly lists is one of my nightmares.

Thanks
Srini










--- "James W. MacDonald" <jmacdon at med.umich.edu>
wrote:

> Hi Srini,
> 
> Srinivas Iyyer wrote:
> > Dear group, 
> > in sigPathway package, authors used 
> > muscle data. 
> > 
> > when one loads:
> > library(sigPathway)
> > data(MuscleExample)
> > I see a "G" object which is nothing but a lit of
> all
> > genes. 
> > 
> >> G[1]
> > [[1]]
> > [[1]]$src
> > [1] "GO:0030054"
> > 
> > [[1]]$title
> > [1] "cell junction"
> > 
> > [[1]]$probes
> >   [1] "220519_s_at" "206083_at"   "204455_at"  
> > "212253_x_at"
> > 
> > 
> > I get clueless in R with list operations. 
> > 
> > How can I make my own sets mimicking "G" list
> object. 
> 
> Well, it depends on what you are starting with. Do
> you have an Affy 
> chip? Illumina? Did you roll yer own?
> 
> Without knowing where you are starting I don't think
> anybody can help you.
> 
> Also note that the authors seem to have a bunch of
> these lists already 
> made that you can download from their site. Have you
> looked there to see 
> if they already made what you want?
> 
> Best,
> 
> Jim
> 
> 
> > 
> > Thank you .
> > srini
> > 
> > 
> >      
>
____________________________________________________________________________________
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> > 
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> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 



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