[BioC] How can I make genesets for sigpathway
srini_iyyer_bio at yahoo.com
Fri Feb 29 16:55:13 CET 2008
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
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.(
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
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
Simply, I dont know how to make an object equivalent
"Genesets_EntrezGeneIDs.RData" is an R workspace
containing Entrez GeneIDs corresponding to gene sets
from GO, KEGG, and other pathway databases.
egidDir <- getwd()
 "C:/Documents and Settings/srini/My
> biocAnnot <- "rat2302"
> library(biocAnnot, character.only = TRUE)
Error in library(biocAnnot, character.only = TRUE) :
there is no package called 'rat2302'
 "biocAnnot" "egidDir" "G.EGIDs"
> xx <- as.list(get(paste(biocAnnot, "ENTREZID", sep =
Error in get(paste(biocAnnot, "ENTREZID", sep = "")) :
R version 2.6.1 (2007-11-26)
attached base packages:
 stats graphics grDevices utils datasets
other attached packages:
loaded via a namespace (and not attached):
 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.
--- "James W. MacDonald" <jmacdon at med.umich.edu>
> 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
> > genes.
> >> G
> > []
> > []$src
> >  "GO:0030054"
> > []$title
> >  "cell junction"
> > []$probes
> >  "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
> 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?
> > Thank you .
> > srini
> > Be a better friend, newshound, and
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> James W. MacDonald, M.S.
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
Be a better friend, newshound, and
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