[BioC] Several questions goCluster and GOstats...

[Lourdes Peña Castillo]

Hello Everyone,

I am trying to use GO for statistical analysis and I have several
questions which I hope you could help me to answer.

1. How can I change configuration parameters from a goCluster object
without running again config(goCluster_object)?  Alternatively, where
could I find documentation about doing this? For example, I would like
to try different similarity measures  or  different pvalue cut-offs,
etc.
In the manual, it is showed how to change the visualization method so
I assumed there is a slot for all other parameters.

2. goCluster will show only the most significant GO terms (with the
lowest p-value) if there are overlaps.  Is there a way to see all
selected GO terms  (and their p-value), similar to GOHyperG output?

3.  Suppose I use GOHyperG to select the GO terms for a  determined
set of genes,  can I use goCluster for visualization? if yes, how?

4. Is the code for the examples described in the vignette "Using GO
for statistical analyses" available?

5. How can I get the locusLink ID for yeast genes? I would like to use
GOHyperG but I have only ORF and gene names for yeast (and this is not
microarray data). If I use lookUp(myGenes, "YEAST", "GO") I get the GO
Annotations for those genes, but

GOHyperG(myGenes, lib = "YEAST", what = "BP")

doesn't work since there is not YEASTLOCUSID in YEAST.  Do I have to
build an annotation package?

Thanks a lot!

Lourdes