Yeast annotations
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@devarajan-karthik-1385
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.6 years ago
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Devarajan, Karthik wrote: > Hello, > > I'm trying to apply enrichment analyses to gene lists obtained from > yeast data using GOstats. I want to use the Yeast GO slim annotation to > do the analysis. My yeast data is from the SGD database and it is not > clear to me which annotation package I should use. The package > org.Sc.sgd.db is not supported yet and the YEAST package does not seem > to contain the required probe names. Does anyone have any idea what > FIXME (mentioned in the Bioconductor help file for YEAST) refers to? I'd > appreciate any input regarding this issue. > > Thanks, > K > > > > > > > > > [[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 > > Hi Karthik, I would like to try and help you but I need a lot more information. What is your sessionInfo()? And what specifically is not supported that you want to do? In general I recommend for people to use the newer org.Sc.sgd.db packages for organism based annotations. These packages should emulate all the same functionality as the older annotations packages that they are replacing (in this case YEAST is being replaced by org.Sc.sgd.db). Marc
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.6 years ago
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Hi Karthik, Can I further ask what you are using for gene identifiers here? If you are using something other than yeast systematic names, then I suspect you will have trouble. These are the yeast IDs that look like: "YAL001C", or "YGR116W". On a related note, I will correct the error you found in the vignette so that it will state that you are supposed to use yeast systematic names with the YEAST package. Does this help? Marc
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.6 years ago
United States
Devarajan, Karthik wrote: > Hi Mark, > > I was using the gene identifiers from the SGD - they look like S000001, > S000002 etc. I have now been able to map these to corresponding yeast > ids and it's working! > > Thanks very much for your help with this. > > Do you know when org.Sc.sgd.db will be supported? > > Best, > Karthik > Hi Karthik, I am glad to hear that you found out what the problem was and that everything is working now. As for your question about the org.Sc.sgd.db, I can't know for sure because you never posted enough of an example for me to replicate everything that you were doing. But in the email you sent to me before you had this: > params <- new("GOHyperGParams", geneIds=gene.id, universeGeneIds=gene.all, annotation="org.SC.sgd.db", ontology="CC", pvalueCutoff=hgCutoff,conditional=FALSE, testDirection="over") > hgOver <- hyperGTest(params) Error: getAnnMap: package org.SC.sgd not available And THAT will definitely not work just because the actual package is called "org.Sc.sgd.db" and not "org.SC.sgd.db"... The "org.Sc.sgd.db" package should have everything in it that you would find in the "YEAST" package. So I would be surprised if that package does not work for you here as well. Marc
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