Question: issues with the hypergeometric test for gene enrichment analysis
0
gravatar for Marouen Ben Guebila
2.9 years ago by
Luxembourg
Marouen Ben Guebila0 wrote:

Hello everyone, I am trying to perform gene enrichment analysis of a set of genes. The test I have used in matlab is the hypergeometric probability density function. The issue is that I noticed that some pathways had a significant p-values although they had 0 genes counted. Thanks for your help.

ADD COMMENTlink modified 2.8 years ago by EagleEye6.2k • written 2.9 years ago by Marouen Ben Guebila0

Are you doing a two-sided test? You likely don't want to do that.

ADD REPLYlink written 2.9 years ago by Devon Ryan89k

Actually, I thought about that, though the matlab function hygepdf, nor the r function dhyper have the argument for one sided test. https://stat.ethz.ch/R-manual/R-devel/library/stats/html/Hypergeometric.html

ADD REPLYlink written 2.9 years ago by Marouen Ben Guebila0
2

I assume that there's an equivalent of the R fisher.test function in matlab. Try using that and seeing if the results differ. Fisher's test is the same thing but will involve less reinvention of the wheel.

ADD REPLYlink written 2.9 years ago by Devon Ryan89k

Devon, maybe you can help with the following situation I have a list of upregulated genes, and I've downlaoded GO pathways in my system. How can I proceed? I am aware of the tools available out there, I am not intending to reinvent the wheel it is just part of a pipeline. thanks!

ADD REPLYlink written 2.9 years ago by Marouen Ben Guebila0
2

As WouterDeCoster aptly wrote, don't reinvent the wheel. There are many many packages already existing to do GO analysis, just use one. You'll likely need to stop using matlab for this, but that's no loss (it's rather uncommonly used in bioinformatics).

ADD REPLYlink written 2.9 years ago by Devon Ryan89k
1

I think there are many tools you can just plug in to your pipeline, rather than as you say reinvent the wheel. (e.g. topGO in R)

ADD REPLYlink written 2.9 years ago by WouterDeCoster38k
0
gravatar for EagleEye
2.8 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

Use this simple tool, no installation required, easy to integrate as part of any pipeline,

Gene Set Clustering based on Functional annotation (GeneSCF)

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by EagleEye6.2k
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