Question: Several questions goCluster and GOstats...
14.1 years ago by
Lourdes Peña Castillo • 140
Lourdes Peña Castillo • 140 wrote:
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
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