Question: Using Gostats on a new organism
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gravatar for January Weiner
9.4 years ago by
January Weiner370 wrote:
Dear all, I am fighting with the GOStats vignettes and the corresponding chapters from the Springer books, and I'm lost. I have a genome (and corresponding arrays) of an organism, along with GO assignments. I'd like to run an enrichment analysis. GOStats seems to need the db packages, is that correct? Is there another way of running it? I would be grateful for any links or hints for further reading. Best regards, January P.S. I'd like to thank here for all who have helped me before; I don't want to clutter the discussions with countless "thank you" e-mails :-) -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514
organism gostats • 640 views
ADD COMMENTlink modified 9.4 years ago by michael watson IAH-C3.4k • written 9.4 years ago by January Weiner370
Answer: Using Gostats on a new organism
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gravatar for michael watson IAH-C
9.4 years ago by
michael watson IAH-C3.4k wrote:
Hi This may not help you with GOstats, but we have example code on our website on how to use topGO: http://bioinformatics.iah.ac.uk/sample-code Thanks Mick ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of January Weiner [january.weiner @mpiib-berlin.mpg.de] Sent: 15 June 2010 11:19 To: BioC Subject: [BioC] Using Gostats on a new organism Dear all, I am fighting with the GOStats vignettes and the corresponding chapters from the Springer books, and I'm lost. I have a genome (and corresponding arrays) of an organism, along with GO assignments. I'd like to run an enrichment analysis. GOStats seems to need the db packages, is that correct? Is there another way of running it? I would be grateful for any links or hints for further reading. Best regards, January P.S. I'd like to thank here for all who have helped me before; I don't want to clutter the discussions with countless "thank you" e-mails :-) -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514 _______________________________________________ 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
ADD COMMENTlink written 9.4 years ago by michael watson IAH-C3.4k
Hello January, GOstats mostly use the db packages, but it's also possible to use it without, as long as you have you own gene-to-GO mappings (can be downloaded from e.g. Ensembl vis biomaRt in many cases). Have a look at the vignette "GOstatsForUnsupportedOrganisms.pdf" at http:// www.bioconductor.org/packages/release/bioc/html/GOstats.html HTH \Heidi On 15 Jun 2010, at 11:31, michael watson (IAH-C) wrote: > Hi > > This may not help you with GOstats, but we have example code on our > website on how to use topGO: > > http://bioinformatics.iah.ac.uk/sample-code > > Thanks > Mick > ________________________________________ > From: bioconductor-bounces at stat.math.ethz.ch [bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of January Weiner > [january.weiner at mpiib-berlin.mpg.de] > Sent: 15 June 2010 11:19 > To: BioC > Subject: [BioC] Using Gostats on a new organism > > Dear all, > > I am fighting with the GOStats vignettes and the corresponding > chapters from the Springer books, and I'm lost. > > I have a genome (and corresponding arrays) of an organism, along with > GO assignments. I'd like to run an enrichment analysis. GOStats seems > to need the db packages, is that correct? Is there another way of > running it? > > I would be grateful for any links or hints for further reading. > > Best regards, > > January > > P.S. I'd like to thank here for all who have helped me before; I don't > want to clutter the discussions with countless "thank you" e-mails :-) > > -- > -------- Dr. January Weiner 3 -------------------------------------- > Max Planck Institute for Infection Biology > Charit?platz 1 > D-10117 Berlin, Germany > Web : www.mpiib-berlin.mpg.de > Tel : +49-30-28460514 > > _______________________________________________ > 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
ADD REPLYlink written 9.4 years ago by Heidi Dvinge2.0k
Many thanks to you both -- although I cannot directly use Biomart, both topGO and GOStats seem to be a viable alternative. Best regards, j. On Tue, Jun 15, 2010 at 12:31 PM, michael watson (IAH-C) <michael.watson at="" bbsrc.ac.uk=""> wrote: > Hi > > This may not help you with GOstats, but we have example code on our website on how to use topGO: > > http://bioinformatics.iah.ac.uk/sample-code > > Thanks > Mick > ________________________________________ > From: bioconductor-bounces at stat.math.ethz.ch [bioconductor- bounces at stat.math.ethz.ch] On Behalf Of January Weiner [january.weiner at mpiib-berlin.mpg.de] > Sent: 15 June 2010 11:19 > To: BioC > Subject: [BioC] Using Gostats on a new organism > > Dear all, > > I am fighting with the GOStats vignettes and the corresponding > chapters from the Springer books, and I'm lost. > > I have a genome (and corresponding arrays) of an organism, along with > GO assignments. I'd like to run an enrichment analysis. GOStats seems > to need the db packages, is that correct? Is there another way of > running it? > > I would be grateful for any links or hints for further reading. > > Best regards, > > January > > P.S. I'd like to thank here for all who have helped me before; I don't > want to clutter the discussions with countless "thank you" e-mails :-) > > -- > -------- Dr. January Weiner 3 -------------------------------------- > Max Planck Institute for Infection Biology > Charit?platz 1 > D-10117 Berlin, Germany > Web ? : www.mpiib-berlin.mpg.de > Tel ? ? : +49-30-28460514 > > _______________________________________________ > 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 > -- -------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web : www.mpiib-berlin.mpg.de Tel : +49-30-28460514
ADD REPLYlink written 9.4 years ago by January Weiner370
Hello everyone, If you cannot find a .db package for your model organism of choice, then you might want to look at the vignette titled "Hypergeometric tests for less common model organisms" in the GOstats package. You can see this vignette online right here: http://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/in st/doc/GOstatsForUnsupportedOrganisms.pdf Marc On 06/15/2010 06:12 AM, January Weiner wrote: > Many thanks to you both -- although I cannot directly use Biomart, > both topGO and GOStats seem to be a viable alternative. > > Best regards, > > j. > > On Tue, Jun 15, 2010 at 12:31 PM, michael watson (IAH-C) > <michael.watson at="" bbsrc.ac.uk=""> wrote: > >> Hi >> >> This may not help you with GOstats, but we have example code on our website on how to use topGO: >> >> http://bioinformatics.iah.ac.uk/sample-code >> >> Thanks >> Mick >> ________________________________________ >> From: bioconductor-bounces at stat.math.ethz.ch [bioconductor- bounces at stat.math.ethz.ch] On Behalf Of January Weiner [january.weiner at mpiib-berlin.mpg.de] >> Sent: 15 June 2010 11:19 >> To: BioC >> Subject: [BioC] Using Gostats on a new organism >> >> Dear all, >> >> I am fighting with the GOStats vignettes and the corresponding >> chapters from the Springer books, and I'm lost. >> >> I have a genome (and corresponding arrays) of an organism, along with >> GO assignments. I'd like to run an enrichment analysis. GOStats seems >> to need the db packages, is that correct? Is there another way of >> running it? >> >> I would be grateful for any links or hints for further reading. >> >> Best regards, >> >> January >> >> P.S. I'd like to thank here for all who have helped me before; I don't >> want to clutter the discussions with countless "thank you" e-mails :-) >> >> -- >> -------- Dr. January Weiner 3 -------------------------------------- >> Max Planck Institute for Infection Biology >> Charit?platz 1 >> D-10117 Berlin, Germany >> Web : www.mpiib-berlin.mpg.de >> Tel : +49-30-28460514 >> >> _______________________________________________ >> 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 >> >> > > >
ADD REPLYlink written 9.4 years ago by Marc Carlson7.2k
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