[BioC] How can I make genesets for sigpathway

[James W. MacDonald]

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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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
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