tag:blogger.com,1999:blog-1861070732189366413.post5698315574392936978..comments2022-03-31T02:28:16.703-07:00Comments on R Chronicle: Another look at over-representation analysis interpretationUnknownnoreply@blogger.comBlogger4125tag:blogger.com,1999:blog-1861070732189366413.post-30324764252345133232013-03-25T06:50:11.472-07:002013-03-25T06:50:11.472-07:00GOTERM is an annotation object part of the GO.db p...GOTERM is an annotation object part of the GO.db package. This package is loaded automatically through a call for GOstats if you use the GO_over function.<br />just load the GOstats library and it should be fine.Anonymoushttps://www.blogger.com/profile/05028598757952012745noreply@blogger.comtag:blogger.com,1999:blog-1861070732189366413.post-91263704146982801892013-03-25T06:08:38.227-07:002013-03-25T06:08:38.227-07:00Hi David,
Thanks for a good post.
I tried to run ...Hi David,<br /><br />Thanks for a good post.<br />I tried to run your script on my own data, however I get an error when I try to create the goNames object (line 25 in your heatmap script). I'm sure I missed something, but I haven't been able to figure out what "GOTERM' refers to in your mget() command. Could you maybe point me in the right direction?<br /><br />Many thankspkd188https://www.blogger.com/profile/13787052365030243569noreply@blogger.comtag:blogger.com,1999:blog-1861070732189366413.post-84163374346329891602012-05-31T05:30:46.232-07:002012-05-31T05:30:46.232-07:00Hi David,
Another plug for Enrichment Map. I don&...Hi David,<br /><br />Another plug for Enrichment Map. I don't use the plugin directly, but the principle is easy to implement, and is related to your idea of using the degree of gene overlap between the annotations to organize them. It is pretty trivial to create a network of terms, and use the RCytoscape package to visualize the network interactively in Cytoscape. I actually used this methodAnonymoushttps://www.blogger.com/profile/11732353840939638830noreply@blogger.comtag:blogger.com,1999:blog-1861070732189366413.post-21302388847197210292012-05-24T10:32:47.738-07:002012-05-24T10:32:47.738-07:00Hey David,
I suggest you check out Enrichment Ma...Hey David, <br /><br />I suggest you check out Enrichment Map (http://www.baderlab.org/Software/EnrichmentMap) Although originally developed for visualization of GSEA results, it works with DAVID enrichment results as well. It creates a network of terms and connects them based on the amount of genes shared between them. It's pretty to look at as well.Anonymousnoreply@blogger.com