Hi Bucher,
 
Thanks for the information. I got an error after I tried to use KEGG.db. Here is what I did:
 
>ids <- scan("D:/geneset.txt")
> ids
 [1] 944750 944834 944794 944854 947139 947874 944866 945013 944925 945017 945081 945070
>pathway <- mget(ids,KEGGEXTID2PATHID, ifnotfound = NA)
Error in .checkKeysAreWellFormed(keys) : 
  keys must be supplied in a character vector with no NAs

Can you help? Thanks!
 
Chen, Yue
 

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Today's Topics:

   1. how to get gene list after hyperGTest (Yue, Chen - BMD)
      (Bucher Elmar)


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Message: 1
Date: Mon, 21 Dec 2009 11:53:56 +0200
From: Bucher Elmar <Ext-Elmar.Bucher@vtt.fi>
Subject: [BioC] how to get gene list after hyperGTest (Yue, Chen -
        BMD)
To: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch>
Message-ID:
        <94C37E6FD527C443B24CA58F2CCBC6C2C433D5D52E@VTTMAIL.ad.vtt.fi>
Content-Type: text/plain; charset="us-ascii"

Hi Chen Yue,

To link genes to KEGG pathways try out this package:
http://www.bioconductor.org/packages/2.5/data/annotation/html/KEGG.db.html

KEGG.db is a AnnotationDbi package. Many kind of Metadata information is stored in such AnnotationDbi packages. So, if you understand to come along whit one AnnotationDbi you will be able to handle all the other AnnotationDbi. AnnotationDbi packages always end by ".db" in their name. 


To get you started:

# install the package
source("http://bioconductor.org/biocLite.R")
biocLite("KEGG.db")

# attach the package
library(KEGG.db)

# some man pages
?KEGG.db    # basic man page
? ls("package:KEGG.db")    # list all the object that exist in KEGG.db
?"KEGGEXTID2PATHID"    # maybe the object you where looking for

# some example
ids <- c("7150","1281542","1274031")
pathway = mget(ids, KEGGEXTID2PATHID, ifnotfound = NA)
pathway


Ps: This is what is written on the bioconductor homepages about AnnotationDbis ( http://www.bioconductor.org/overview ) :
The Bioconductor project provides software for associating microarray and other g0enomic data in real time to biological metadata from web databases such as GenBank, LocusLink and PubMed (annotate package). Functions are also provided for incorporating the results of statistical analysis in HTML reports with links to annotation WWW resources.
Software tools are available for assembling and processing genomic annotation data, from databases such as GenBank, the Gene Ontology Consortium, LocusLink, UniGene, the UCSC Human Genome Project (AnnotationDbi package).
Data packages are distributed to provide mappings between different probe identifiers (e.g. Affy IDs, LocusLink, PubMed). Customized annotation libraries can also be assembled.

Merry Christmas, Elmar



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Today's Topics:

   1. how to get gene list after hyperGTest (Yue, Chen - BMD)


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Message: 1
Date: Sat, 19 Dec 2009 12:36:26 -0600
From: "Yue, Chen - BMD" <yuechen@bsd.uchicago.edu>
Subject: [BioC] how to get gene list after hyperGTest
To: <bioconductor@stat.math.ethz.ch>
Message-ID:
        <AD1FA15416EEBC49A0FE4F8B0C8AD7C5158F35@ADM-EXCHVS04.bsdad.uchicago.edu>
       
Content-Type: text/plain

Hi,

I'm wondering if someone can help me with the result extraction after hyperGTest in GOstats package. After I obtained the hyperGTest result, I also want to know what category each input gene associates with, for example a KEGG pathway. What function should I use? Or should I use another package?

Thanks!

Chen, Yue



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