p-values in Reactome and ReactomePA
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@heir_of_isildur88-15346
Last seen 17 months ago

Hi all,

I am using Reactome for GO / Pathway Enrichment analysis for my set of DE genes. Besides the web interface, I am also using the ReactomePA R package for the analysis. I am confused with the settings & p-values for these 2.

1) In the Reactome web interface, the results show an entities p-value - is this p-value adjusted or not? 

2) Should I use the p-value or adjusted p-value to check my DE genes? When I analyze it in ReactomePA by adjusting the pAdjustMethod, I got different results for none adjusted and bonferonni adjusted. 

Could someone please advise?

Thank you very much.

reactomepa reactome • 869 views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

for 2nd issue

the result is expected to be different since the p value adjustment rely on the whole set of pvalues while in the 'do it yourself' only a subset was used.


 

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So which set of pathways should I actually use as my result? The ones found using the adjusted p-value or the one without?

I am still confused about this p-value thing and the difference between the web Reactome and your ReactomePA package. What is the difference in the method of p-value calculation in the web Reactome and your package? I read somewhere that the p-value in Reactome is calculated using the BH method, but why does the p-values differ with the ones from ReactomePA even when I use the similar pvalueAdjustMethod?

Sorry but I am quite new to this type of analysis. I read up on p-value adjustment but still have some difficulty understanding it. Could you please explain all my queries in a simple manner? 

Thank you very much.

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