[BioC] Visualizing GOstats HyperGTest results

Srinivas Iyyer srini_iyyer_bio at yahoo.com
Sun Jan 20 07:58:33 CET 2008

Dear Group, 
Apologies for a similar re-post on this issue. 

I kindly want to bring to the attention of
bioconductor developers, if there is a function to
generate a heatmap of all enriched GO categories after
a conditional hyperGTest.  

For example, I have 5 different time points
time-series data and with 3 different doses. I run
HyperGTest and I endup with atleast 50 categories for
5 time points and 3 drug treatments. 

3hr @ d1; 3hr @ D2 ; 3 hr @ D3 - 50, 50 ,50 cats

Like wise for 6 and 12 hrs for D1,D2 and D3. 

I have finally many HTML tables after testing for all
time points and drugs. 

If I have a function to generate a heatmap for D1
all 3 time points on X-axis and a union of enriched
categories on Y-axis and color them according to FDR
or P-values, it would be a nice visualization. If
somehow I can plot all timepoints and all drug effects
along with GO categories, that would be a beautiful
depiction of results. 

my questions are:

1. Is there an inbuilt GOstats function like
that.(goCluster has something similar, however it is
not as easy to combine for a basic R skillset person
like me).

2. If not, is it possible to combine all results and
use standard heatmap function to obtain a figure of
what I wanted and described above. 

I appreciate if any one can suggest or help me in this

thank you. 



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