Up- or down- regulated pathways or GO terms?
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affy snp ▴ 640
@affy-snp-2480
Last seen 8.4 years ago
Hi all, I wonder whether there is any tool which can demonstrate up- or down- regulation of pathways or GO terms in a plot when doing microarray analysis? Thanks a lot! Allen [[alternative HTML version deleted]]
Microarray Pathways GO Microarray Pathways GO • 895 views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 6.5 years ago
United States
Hi Allen, You might want to look at the GOstats and Category packages. http://www.bioconductor.org/packages/devel/bioc/html/GOstats.html http://www.bioconductor.org/packages/devel/bioc/html/Category.html These packages are meant to be used after you have some genes that you feel are interesting (possibly based on results from a microarray experiment). Marc ss wrote: > Hi all, > > I wonder whether there is any tool which can demonstrate up- or down- > regulation > of pathways or GO terms in a plot when doing microarray analysis? > > Thanks a lot! > > Allen > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >
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@michael-watson-iah-c-378
Last seen 8.4 years ago
KEGGSOAP is also an excellent package for colouring pathways by numerical values. I have some demo code for that if you need it Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Marc Carlson Sent: Mon 06/04/2009 6:05 PM To: ss Cc: BioC Subject: Re: [BioC] Up- or down- regulated pathways or GO terms? Hi Allen, You might want to look at the GOstats and Category packages. http://www.bioconductor.org/packages/devel/bioc/html/GOstats.html http://www.bioconductor.org/packages/devel/bioc/html/Category.html These packages are meant to be used after you have some genes that you feel are interesting (possibly based on results from a microarray experiment). Marc ss wrote: > Hi all, > > I wonder whether there is any tool which can demonstrate up- or down- > regulation > of pathways or GO terms in a plot when doing microarray analysis? > > Thanks a lot! > > Allen > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > _______________________________________________ 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
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Hi Mick, I am also interested in your demo code to compare pathways. Thanks Narendra >> "michael watson (IAH-C)" <michael.watson at="" bbsrc.ac.uk=""> 06/04/2009 18:11 >>> KEGGSOAP is also an excellent package for colouring pathways by numerical values. I have some demo code for that if you need it Mick - ss wrote: > Hi all, > > I wonder whether there is any tool which can demonstrate up- or down- > regulation > of pathways or GO terms in a plot when doing microarray analysis? > > Thanks a lot! > > Allen > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > > _______________________________________________ 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 _______________________________________________ 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
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Paolo Sonego ▴ 140
@paolo-sonego-3256
Last seen 8.4 years ago
Italy
Hi Michael, I also would like to to take a look at your demo code. Regards, Paolo
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