GOstats Annotation Package
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Jörg ▴ 40
@jorg-3228
Last seen 9.8 years ago
Hello, is there any way to build an annotation package usable with GOstats on your own??? I don't have any Microarray data but I still want to use Gostats to look for overrepresented terms in some gene lists. I would like to build an annotation package using the annotations from GO homepage directly. Is there any way? I know this is possible with topGO but there is no conditional hypergeometric test, is it? Thanks for your answer! J?rg --
Microarray Annotation GOstats topGO Microarray Annotation GOstats topGO • 1.4k views
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@joern-toedling-1244
Last seen 9.8 years ago
Hello, there are functions in the AnnotationDbi package for building custom ".db" annotation packages. See the vignette "SQLForge" in that package for details. This functionality is meant to supersede the AnnBuilder package, which could be used to generate annotation package of the previous generation. The package topGO allows for such a test without requiring an annotation package. Similar to the conditional hypergeometric test, topGO also includes variants of the hypergeometric test that take the structure of the GO into account. See the paper by Alexa et al. (2006) for details: http://bioinformatics.oxfordjournals.org/cgi/content/full/22/13/1600 Regards, Joern J?rg Linde wrote: > Hello, > is there any way to build an annotation package usable with GOstats on your own??? I don't have any Microarray data but I still want to use Gostats to look for overrepresented terms in some gene lists. I would like to build an annotation package using the annotations from GO homepage directly. > Is there any way? > I know this is possible with topGO but there is no conditional hypergeometric test, is it? > > Thanks for your answer! > J?rg > -- >
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