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List:       bioconductor
Subject:    [BioC] Post hyperGTest : drawing GO graphs
From:       "balag Ganesan" <bala.g () aggiemail ! usu ! edu>
Date:       2008-09-29 18:52:58
Message-ID: e8994d720809291152nfb3f3c7w3bc3c2bd48d5dd77 () mail ! gmail ! com
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Dear allI have been working recently on drawing GO graphs of the
significantly changing GOs, and have extensively used the instructions for
the packages GOstats and TopGO for drawing the post-analysis results
(hyperGTest or Fisher's test, respectively) for drawing the GO graphs. I am
trying to do this for some yeast data that we collected in a previous
project.
Unfortunately the functions in or connected to both packages seem to draw
the DAGs for only the significant GOs and their connected GOs, and do not
allow me to highlight the significant categories on the complete GO DAG for
each ontology (CC, BP, or MF).
After extensive searches and failure to find something on the Bioconductor
forums about this I have chosen to request help.
Could somebody please provide me more guidance on how to draw a full GO DAG
in R with only significant ones highlighted? An older forum thread that
specifically deals with this issue would immensely help, as well as
suggestions on how to do this.
I am aware that there are a selected number of web-based tools that offer
the capabilities but I do not always work online and am sometimes limited by
sporadic web access. The ability to do this locally will help substantially.
I am currently running R2.7.2 on a MacOSX 10.4.11 PPC.
I am happy to provide more information if needed to help me make this work.
Any help is highly appreciated.
Thank you
Regards
BALA.

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