Question: How To Combine P-Values Obtained With Different Approaches?
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gravatar for J.F.Jiang
6.5 years ago by
J.F.Jiang750
China
J.F.Jiang750 wrote:

Hi ALL,

I am stacked by a problem of how to combine different p values.

I just got 3 different pvalues using different method, for example chisq test, logistic regression, how can I obtain the combined p? one possible way reported was to convert the p value to z value first and then calculate the final p, is there any other possible method?

Another similar question is that suppose I got 2 GWAS datasets of the same population but different genotype platform though using imputation process, the p value for the same SNP would be different, so how can i combine this kind of p? I know meta can do this kind of thing, but since there is only two datasets, which will lead to impossible for meta analysis

So if anyone knows any method that can fix this kind of problem, could you plz tell me the reference?

Thanks a lot!

Added: not on the same datasets, for example, using a gene expression dataset, I can obtain the p value for a specific gene, meanwhile, using a gwas dataset, I can assign the p-value of most significant SNP to this gene. My question is how to combine these kind of p-values to obtain the updated p-value for this gene?

gwas • 4.8k views
ADD COMMENTlink modified 6.2 years ago by lyz10302012330 • written 6.5 years ago by J.F.Jiang750
1
gravatar for Manu Prestat
6.5 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

You don't want to merge p-values sets obtained by testing different statistical models. If you want to see if 3 different statistics give you similar answers, you can check if they agree by drawing a Venn diagram. I can not tell you more about multi-platform SNP analysis though...

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Manu Prestat3.9k

not on the same datasets, for example, using a gene expression dataset, I can obtain the p value for a specific gene, meanwhile, using a gwas dataset, I can assign the p-value of most significant SNP to this gene. My question is how to combine these kind of p-values to obtain the updated p-value for this gene?

ADD REPLYlink written 6.5 years ago by J.F.Jiang750
0
gravatar for Andreas
6.5 years ago by
Andreas2.4k
Singapore
Andreas2.4k wrote:

EDIT: please see Sean's comment below. Keeping my answer here only for the sake of completeness/discussion.

You might want to look at Fisher's method.

Andreas

ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by Andreas2.4k
2

Note that Fisher's method is an approach for combining p-values, but it is usually applied in the setting of different dataset, not for multiple p-values from the different tests on the same datasets, as Manu points out.

ADD REPLYlink written 6.5 years ago by Sean Davis25k

not on the same datasets, for example, using a gene expression dataset, I can obtain the p value for a specific gene, meanwhile, using a gwas dataset, I can assign the p-value of most significant SNP to this gene. My question is how to combine these kind of p-values to obtain the updated p-value for this gene?

ADD REPLYlink written 6.5 years ago by J.F.Jiang750
0
gravatar for Maxime Lamontagne
6.5 years ago by
Québec
Maxime Lamontagne2.1k wrote:

For your GWAS problem, use the Fisher's method for meta-analysis: http://en.wikipedia.org/wiki/Fisher%27s_method

ADD COMMENTlink written 6.5 years ago by Maxime Lamontagne2.1k
0
gravatar for lyz10302012
6.2 years ago by
lyz10302012330
China
lyz10302012330 wrote:

Did you find your answer? I don't think Fisher's method works for your problem. Your problem tends to accept the max P value, but Fisher's method tends to accept min P Value. Any comment?

ADD COMMENTlink written 6.2 years ago by lyz10302012330
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