[BioC] How can I make genesets for sigpathway

[James W. MacDonald]

Hi Srini,

Srinivas Iyyer wrote:
> 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.

Well, I think this will be way too complicated for anyone to help you 
with via a listserv.

> 
> 
> 
> 
> 
> 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'

So the error ^^^^^^^^^^^^ right there indicates you don't have this 
package installed yet.

>> biocAnnot
> [1] "rat2302"
>> ls()
> [1] "biocAnnot" "egidDir"   "G.EGIDs"  
>> xx <- as.list(get(paste(biocAnnot, "ENTREZID", sep =
> "")))
> Error in get(paste(biocAnnot, "ENTREZID", sep = "")) :

Since the package isn't installed, you will not be able to get anything 
from it.

Anyway, if you want to do something this complicated (e.g., not just 
using the sigPathways package as intended) then you will likely have to 
get help from the authors to make your own G.EGIDs list. On the webpage 
you reference at the bottom it says to contact Peter J. Park if you have 
questions. I think probably that is the best way to go.

Best,

Jim


> 
>> 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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>> -- 
>> 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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-- 
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