Question: topGO - treating up- and down-regulated genes separately
gravatar for predeus
20 months ago by
United States
predeus0 wrote:

I've recently started using topGO in my expression analysis and like it a lot. The "elimination" paradigm is a very useful one when doing pathway analysis, since many different pathways do in fact overlap in the genes they contain. 

In the manual, all the examples are using p-values as a statistic, but never separate the up- and down-regulated genes. They should be considered separately, should they not? 

And, correspondingly, would it be necessary to modify the application for Kolmogorov-Smirnov statistic and KS-elim? In classical GSEA, your statistic has a plus or a minus sign, to indicate if the gene is up- or down-regulated. However, since you're only using the p-values, I was curious as to how can you separate them. 

Additionally, it would be nice to understand how are the p-values used in Kolmogorov-Smoirnov (like) methods in topGO, and whether it is possible to use another statistic - such as t-statistic from limma or Wald statistic from DESeq2. 

ADD COMMENTlink modified 20 months ago by Lluís Revilla Sancho430 • written 20 months ago by predeus0
gravatar for Lluís Revilla Sancho
20 months ago by
European Union
Lluís Revilla Sancho430 wrote:

One can use any statistic you want. The statistic is used to select the genes with geneSelectionFun.(Be aware that geneSelectionFun doesn't work properly).


However I can't shed any light to how are the p-values calculated (You can have a p-value of a GO term without any significant gene on that term, how? I don't know).

ADD COMMENTlink written 20 months ago by Lluís Revilla Sancho430

yeah, it's pretty clear how it works for Fisher's statistics and the like - you just select the genes you consider significant and calculate the p-value for 2x2 table

it's much more tricky for KS (or KS-like, as in GSEA) - statistic should add up some statistic (in some power) to the running sum, right? So there's no way to distinguish up- and down-regulated genes - you just lump them all together. 

I think this might be very misleading to a lot of users and produce meaningless results. 

The bug you are describing is also interesting. Did you try reporting it? 

ADD REPLYlink written 20 months ago by predeus0

You can distinguish up and down regulated genes if you use the t statistic or the fold change (or log fold change). How is the statistic used in the KS approach? I am not sure. 

Yes, I reported the bug several times

ADD REPLYlink written 20 months ago by Lluís Revilla Sancho430
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