Dear Seth,

I think that the problem with the documentation is that it assumes 
the user knows more than most of us do.

I was OK with the section on gene filtering, but I think probably 
quite a few people would need instruction on what you mean, and what 
the filtering output should be.

Then, I did not know how to obtain the Entrez of Locus Link ID.  I 
found this on the searchable e-mail archive.

I did not understand that I needed to create params and give it the 
right class, although once I blindly followed the example it was clearer.

As a statistician, I knew what was required for the pvaluecutoff, but 
I think many people would not realize this is the level the enrichment test.

I still am not clear on what the conditional parameter does.

Taking an example from start to finish would help.

I also had a problem using the output once I got it.  The htmlReport 
was fairly clear.  In the end, I figured out that HyperGTest had 
reduced the universeGeneIds to the unique ids (which is great, 
because I forgot to do so) and that the "size" column was the number 
of genes in universeGeneIds-GeneIds that were in the category (from 
the docuentation, I thought it was the number in universeGeneIds).

It would be nice if the documentation also included all the methods 
for the GoHyperGResult class, as I had some trouble extracting output to R.

Anyways, now that I have it working and I got both the table and the 
graph, it is definitely very cool.

For example, given the result of a hyperGtest, one could plot all GO
terms significant at a specified p-value and show their relationships.

That is what I expected to get.  Couldn't that be the default?  If 
not, perhaps the documentation should show how to do this.

Thanks,
Naomi

At 01:24 PM 11/27/2006, Seth Falcon wrote:
>Naomi Altman <naomi@stat.psu.edu> writes:
>
> > I am starting to use GOstat, and there are several things I do not
> > understand.
>
>Please let me know what parts are not clear.  I would like to improve
>the documentation and make the code as easy to use as possible.
>
> > I managed to get output from HyperGTest.  I was able to view the
> > enriched categories using htmlReport.
> >
> > I would like to try out the graphing methods, but I have not been
> > able to figure out the input.  In particular, I assume that since I
> > have created a GOHyperGResult object, I should use
>
>The plot methods in GOstats are not very refined.  In part, this is
>because it isn't always clear what picture one should draw.
>
>So suggestions here would be welcome.
>
>For example, given the result of a hyperGtest, one could plot all GO
>terms significant at a specified p-value and show their relationships.
>But that is a rather incomplete picture.  OTOH, if you expand the
>graph by very much it becomes useless as you can't see anything once
>you plot 100 nodes at once.
>
> > getGoGraph
> >
> > but I have not figured out what goes into the goIds argument.  I
> > presume it is some type of node identifier, but where do I find it?
>
>goIds should be a character vector of GO IDs, like "GO:xxxxxx".
>
>+ seth
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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