Adjusted p-values for ORA analysis

[Agnese Giovannetti]

Dear Webgestalt community, 

I need a clarification on how adjusted p-values are calculated during ORA analysis.

I have a set of genes for which I am performing a disease enrichment (GLAD4U based). When I run the analysis using WebGestaltR, I obtain the enrichment results here attached. However, when I try to calculate, from obtained p-values, the adjusted p-values using R function "p.adjust" (with "BH" method), I do not obtain same adjusted p-values reported in the enrichment results file.

Could you please help me?

This is the code for WebGestaltR

>WebGestaltR(enrichDatabase="disease_GLAD4U",

interestGeneType="genesymbol",

interestGeneFile="myfile.txt",

referenceSet="genome_protein-coding", 

minNum=5, 

maxNum = 200, 

sigMethod="top", 

topThr=1000, 

fdrMethod="BH",

reportNum=1000)

Thanks,

Agnese

[Yuxing Liao]

Hi Agnese,

I think it is likely because you do not have p-values for all gene sets to compare. For example, you probably just adjust p-values for the reported significant gene sets. But the program has to adjust p-values for all gene sets at once.

Yuxing

--
You received this message because you are subscribed to the Google Groups "webgestalt" group.
To unsubscribe from this group and stop receiving emails from it, send an email to webgestalt+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/webgestalt/57921952-2925-457a-b020-6f88191f4f15n%40googlegroups.com.