GOstats Annotation Package
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Jörg ▴ 40
Last seen 9.9 years ago
Dear Joern, I am sorry for the late reply. I just wanted to thank you for your advise. It was extremely helpful. The package "topGo" is exactly what I was looking for. Thank you so much J?rg -------- Original-Nachricht -------- > Datum: Wed, 25 Feb 2009 16:07:53 +0000 > Von: Joern Toedling <toedling at="" ebi.ac.uk=""> > An: "J?rg Linde" <edd17 at="" gmx.de=""> > CC: bioconductor at stat.math.ethz.ch > Betreff: Re: [BioC] GOstats Annotation Package > 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 > > -- > > -- Nur bis 16.03.! DSL-Komplettanschluss inkl. WLAN-Modem f?r nur 17,95 ?/mtl. + 1 Monat gratis!* http://dsl.gmx.de/?ac=OM.AD.PD003K11308T4569a
Microarray Annotation GO GOstats topGO AnnotationDbi Microarray Annotation GO GOstats • 829 views

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