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Question: GO enrichment comparison with other programs
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gravatar for fizer
10 months ago by
fizer30
US
fizer30 wrote:

Hi,

The comparison done in the  "functional enrichment for GTEx paper". I wonder if there is a way to do the comparison using enrichment results that are contained in data.frames? For example, clusterprofiler vs goseq vs topGO.

Thanks

ADD COMMENTlink modified 10 months ago by Guangchuang Yu800 • written 10 months ago by fizer30

Not quite sure why you would bother doing this because these functional enrichment tests/ packages are usually the same and based on hypergeometric distribution, the issue is just using a package that updates its definitions of KEGG or GO pathways etc. I use cluster profiler and find it very helpful.

ADD REPLYlink modified 10 months ago • written 10 months ago by chris86340
1

Hi, they are actually not the same. TopGO (the R package) uses radically different ways of doing the analysis. Taking the structure of the GO-graph into account in different ways to prioritize more specific or informative results. It is quite a good improvement on the traditional hypergeometric approach. TopGO actually does do comparison of the various methods (classical vs. other approaches). But as it says below one can also do it oneself (of course). TopGO is a bit difficult to use though ...

ADD REPLYlink written 10 months ago by Pekka Kohonen190

OK thanks, that is interesting.

ADD REPLYlink written 10 months ago by chris86340

goseq adjusts for gene length bias, which means that the null distribution is not hypergeometric.

ADD REPLYlink modified 10 months ago • written 10 months ago by Gordon Smyth32k
0
gravatar for Guangchuang Yu
10 months ago by
Hong Kong
Guangchuang Yu800 wrote:

combine data.frame and use ggplot2 to visualize.

You need to do it yourself.

 

ADD COMMENTlink written 10 months ago by Guangchuang Yu800
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