[BioC] meta-analysis with P values

[Debashis Ghosh]

I agree with Vince about posting to R-help.  However, if you have
individual P-values, I am not sure
why you cannot do a ordinary meta-analysis combining p-values using
Fisher's method.  There is not an
R package to do this, but it would simply involve calculating

 T = -2*log(p-value1)-2*log(p-value2)-...-2*log(p-valuem)

where m is the number of p-values.  Under the null hypothesis, this
will be distributed as chi-squared
with m degrees of freedom, so you would then do

T.pval = 1-pchisq(T,m)

to get the combined p-value.

HTH,
Debashis

On Wed, Jul 14, 2010 at 11:01 PM, Vincent Carey
<stvjc at channing.harvard.edu> wrote:
> This is really a question for R-help.  However, rmeta could be used if
> you knew the study effect sizes and standard errors (see
> meta.summaries).  Under certain assumptions you would be able to
> derive a standard error for a given estimate from a p-value and sample
> size.
>
> On Wed, Jul 14, 2010 at 3:55 PM, Laura Rodriguez Murillo
> <laura.lmurillo at gmail.com> wrote:
>> Hi dear list,
>>
>> My question is on meta-analysis. I have three studies on the association of
>> a SNP with a disease and I need to do a random-effects meta-analysis with my
>> data. I only have the individual P value, the odds ratio and sample size
>> from each study. I've checked rmeta and meta packages but it seems to me
>> that I need to know the number of observations on each group, which I don't
>> have in this case. Is there any other package I can use that accepts doing
>> meta-analysis with these data?
>>
>> Thanks a lot for your help!
>>
>> Laura
>>
>>        [[alternative HTML version deleted]]
>>
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-- 
Debashis Ghosh
Departments of Statistics and Public Health Sciences
Penn State University
University Park, PA 16802
works.bepress.com/debashis_ghosh/