It didn't work because this pathway are not present. As an example, try to 
change "Biosynthesis of steriods" in this piece of code by "Pyruvate 
metabolism". 

Best;

Gustavo




2005/6/16, Alberto Goldoni <alberto.goldoni@eurogene.org>:
> 
> Sorry but it doesn't work:
> 
> > get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID),
> sep= ""),KEGGPATHID2EXTID)
> Error in get(x, envir, mode, inherits) : variable "Biosynthesis of
> steriods" not find
> 
> -----Messaggio originale-----
> Da: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch] Per conto di John Zhang
> Inviato: giovedì 16 giugno 2005 16.55
> A: michael.auer@meduniwien.ac.at; rhaddad@genetics.wayne.edu
> Cc: bioconductor@stat.math.ethz.ch
> Oggetto: Re: [BioC] Pathway Information
> 
> Suppose you are looking for gene that are involved in human
> "Biosynthesis of
> steriods" pathway, the following will give you a vector of Entrez Gene
> ids:
> 
> >library(KEGG)
> >get(paste("hsa", get("Biosynthesis of steriods", KEGGPATHNAME2ID), sep
> = ""),
> KEGGPATHID2EXTID)
> 
> >X-Original-To: jzhang@jimmy.harvard.edu
> >Delivered-To: jzhang@jimmy.harvard.edu
> >From: Ramsi Haddad <rhaddad@genetics.wayne.edu>
> >To: michael.auer@meduniwien.ac.at
> >Mime-Version: 1.0
> >Date: 16 Jun 2005 09:58:13 -0400
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> >Cc: bioconductor mailing list <bioconductor@stat.math.ethz.ch>
> >Subject: Re: [BioC] Pathway Information
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> autolearn=ham
> version=3.0.1
> >
> >
> >Dear Michael,
> > There is a pretty good description in the globaltest vignette.
> Most of
> >the stuff shown below is based on it:
> >
> >library(mgu74av2)
> >library(KEGG)
> >
> >### this next line generates a list of kegg pathways and all
> >### the probe sets that belong in a given pathway.
> >mouse.kegg.sets <- as.list(mgu74av2PATH2PROBE)
> >
> >### the next 3 lines give the names of the pathways from their
> >### kegg ID numbers
> >all.kegg.ids <- ls(KEGGPATHID2NAME)
> >all.kegg.names <- mget(all.kegg.ids, KEGGPATHID2NAME)
> >table.of.keggs <- as.matrix(unlist(all.kegg.names))
> >write.table(table.of.keggs, "keggs.csv", sep=",",col.names=NA,
> >row.names=T)
> >
> >### here's how to get the name of a given kegg pathway:
> >what.is.00010 <- get("00010", KEGGPATHID2NAME) ## this is glycolysis.
> >
> >### here's how to get the probesets in the Glycolysis Path from the
> >mouse array:
> >glycolysis.affyIDs <- get("00010", mgu74av2PATH2PROBE) ## there are 68
> >such probe sets.
> >another.glycolysis.affyIDs <- mouse.kegg.sets[["00010"]] ## more than
> >one way to skin a cat
> >
> >### here's how to get the kegg pathway numbers for anything with
> >"Cholera"
> >colera.kegg.paths.index <- grep("Cholera", table.of.keggs) ## this
> >provides the index
> >colera.keggs <- table.of.keggs[colera.kegg.paths]
> >### here it is in one step:
> >### table.of.keggs[grep("Cholera", table.of.keggs)]
> >
> >hope that gets you started.
> >
> >Ramsi
> >
> >
> >
> >
> >> Hi
> >>
> >> Can anybody tell me the following
> >>
> >> I want to identify genes which are located on a certain pathway NF
> Kappa.
> >> How can I obtain such an information. Which package is appropriate
> and
> >> which commands are needed. If any body ever encounterd the same
> problem
> >> please let me know.
> >>
> >> Michael
> >--
> >Ramsi Haddad, Ph.D.
> >Center for Molecular Medicine and Genetics.
> >Functional Genomics Laboratory,
> >Perinatology Research Branch, NICHD, NIH.
> >259 Mack Avenue,
> >Room 3146 Applebaum Bldg.
> >Detroit, MI 48201, USA.
> >
> >phone:(313) 577-2569 / fax:(313) 577-7736
> >
> >_______________________________________________
> >Bioconductor mailing list
> >Bioconductor@stat.math.ethz.ch
> >https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> Jianhua Zhang
> Department of Medical Oncology
> Dana-Farber Cancer Institute
> 44 Binney Street
> Boston, MA 02115-6084
> 
> _______________________________________________
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> 



-- 
_______________________________________________________________

"The truth you speak has no past and no future. It is, and 
that's all it needs to be."

"A verdade que você fala não tem passado nem futuro. Ela é, 
e isso é tudo que ela precisa ser."

Autor desconhecido
_______________________________________________________________


Gustavo Henrique Esteves

e-mail: gesteves@gmail.com
Home Page: http://www.vision.ime.usp.br/~gesteves/

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