Question: KEGG package
0
gravatar for Yihuan Xu
11.8 years ago by
Yihuan Xu130
Yihuan Xu130 wrote:
Dear All, I would like to use GSEA to analyze customed microarrays. I need to map genes from ACC number to KEGG pathways. How can I do it using KEGG package? I could not find any documents for KEGG package. Is there any example? Best, Yihuan
pathways • 767 views
ADD COMMENTlink modified 11.8 years ago by John Zhang2.9k • written 11.8 years ago by Yihuan Xu130
Answer: KEGG package
0
gravatar for John Zhang
11.8 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
> >I would like to use GSEA to analyze customed microarrays. I need to map genes from ACC number to KEGG pathways. How can I do it using KEGG package? I could not find any documents for KEGG package. Is there any example? Try the following in R to see if there is anything helpfull: >KEGG() >?KEGG >?KEGGEXTID2PATHID (or any of the environment in KEGG) > >Best, > >Yihuan > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 11.8 years ago by John Zhang2.9k
Hi, Yihuan: Check the following link: http://www.broad.mit.edu/gsea/wiki/index.php/Msigdb_may_2006_release_n otes and you will find KEGG has been built into MsigDB of GSEA. So, if your purpose is GSEA analysis, the only thing you need to do is map your ACC number to Entrezgene id. John's suggestion is also helpful if you try to use KEGG package in BioC. BTW, I recommend you use desktop version of GSEA since it takes me a lot of trouble to change the codes of R's version ( I believe there is a bug and report it to GSEA group already and I believe they are working on that now). HTH, Weiwei On 8/13/07, John Zhang <jzhang at="" jimmy.harvard.edu=""> wrote: > > > > >I would like to use GSEA to analyze customed microarrays. I need to map genes > from ACC number to KEGG pathways. How can I do it using KEGG package? I could > not find any documents for KEGG package. Is there any example? > > > Try the following in R to see if there is anything helpfull: > > >KEGG() > >?KEGG > >?KEGGEXTID2PATHID (or any of the environment in KEGG) > > > > > > > > > >Best, > > > >Yihuan > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jianhua Zhang > Department of Medical Oncology > Dana-Farber Cancer Institute > 44 Binney Street > Boston, MA 02115-6084 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you always know?" "No, I did not. But I believed..." ---Matrix III
ADD REPLYlink written 11.8 years ago by Weiwei Shi1.2k
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