Description
The Gene Ontology (GO) Consortium <https://geneontology.org/> organizes genes into hierarchical categories based on biological process (BP), molecular function (MF) and cellular component (CC, i.e., subcellular localization). Tools such as 'GoMiner' (see Zeeberg, B.R., Feng, W., Wang, G. et al. (2003) <doi:10.1186/gb-2003-4-4-r28>) can leverage GO to perform ontological analysis of microarray and proteomics studies, typically generating a list of significant functional categories. The significance is traditionally determined by randomizing the input gene list to computing the false discovery rate (FDR) of the enrichment p-value for each category. We explore here the novel alternative of randomizing the GO database rather than the gene list.
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Check details (15 non-OK)
examples
Running examples in ‘randomGODB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addName2List
> ### Title: addName2List
> ### Aliases: addName2List
>
> ### ** Examples
>
> BP_ANCESTOR<-addName2List(as.list(GO.db::GOBPANCESTOR))
Error in loadNamespace(x) : there is no package called ‘GO.db’
Calls: addName2List ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
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examples
Running examples in ‘randomGODB-Ex.R’ failed The error most likely occurred in: > ### Name: addName2List > ### Title: addName2List > ### Aliases: addName2List > > ### ** Examples > > BP_ANCESTOR<-addName2List(as.list(GO.db::GOBPANCESTOR)) Error in loadNamespace(x) : there is no package called ‘GO.db’ Calls: addName2List ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted
package dependencies
Package suggested but not available for checking: ‘GO.db’
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Check History
ERROR 12 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE Mar 9, 2026
examples
Running examples in ‘randomGODB-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addName2List
> ### Title: addName2List
> ### Aliases: addName2List
>
> ### ** Examples
>
> BP_ANCESTOR<-addName2List(as.list(GO.db::GOBPANCESTOR))
Error in loadNamespace(x) : there is no package called ‘GO.db’
Calls: addName2List ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
package dependencies
Package suggested but not available for checking: ‘GO.db’