You have addressed the wrong mailing list. See http://www.bioconductor.org/help/mailing-list/ --------------------------------------------------------------------------- Jeff Newmiller The ..... ..... Go Live... DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --------------------------------------------------------------------------- Sent from my phone. Please excuse my brevity.
Asis Hallab <asis.hal...@gmail.com> wrote: >Dear Bioconductor Experts, > >thank you for providing such a useful tool-set. > >I have a question regarding the package AnnotationDbi, specifically >the classes GOFrame and GOALLFrame. > >During a GO Enrichment Analysis I create a data frame with Arabidopsis >thaliana GO annotations and from that first a GOFrame and than from >this GOFrame a GOALLFrame. Checking the result with > >nrow( getGOFrameData( athal.go.all.frame ) ) # The GOAllFrame > >and comparing it with > >nrow( athal.go.frame ) # The >GoFrame > >I realize that the GOALLFrame has more than 5 times more rows than my >original GO annotation table. If I provide >organism='Arabidopsis thaliana' >to the constructor of GOFrame this ratio increases even further. > >Unfortunately I could not find any documentation on this, so I feel >forced to bother you with my questions: > >1) Why does GOALLFrame so many more annotations? >2) Why and from where does it retrieve the organism specific ones that >are added when a model organism like 'Arabidopsis thaliana' is >provided? >3) I suspected that all ancestors of annotated terms are added, but >when I did so myself, I still got less GO term annotations? So do you >add ancestors of the "is_a" type and possibly other relationship types >like "part_of" etc. ? > >Please let me know your answers soon. Your help will be much >appreciated. > >Kind regards! > >______________________________________________ >R-help@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/r-help >PLEASE do read the posting guide >http://www.R-project.org/posting-guide.html >and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
