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unistbig / metapro

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Question about application (not-DEG) #6

Open ericmalekos opened 1 year ago

ericmalekos commented 1 year ago

Thank you for developing this tool and your paper comparing methods. I have a question about applying this method outside of the differentially expressed genes context and would like to know if you see any issues.

I am working with ribosome sequencing (RiboSeq) data to determine whether open reading frames are being actively translated. Translation prediction is based on Wilcoxon rank sum test which counts the in-frame vs. out-of-frame reads as described in this paper. In this way p-values are generated for each ORF against the null-hypothesis that the ORF is not being translated.

Because RiboSeq is typically very shallow (likely to lead to false negatives in this case), I would like to combine the p-values from multiple experimental datasets. Does this seem an appropriate case for your tool?

ysora commented 1 year ago

Hi, Sorry for the late response. I didn't check this GitHub page for a while. I think that is a great application of p-value combining method. If I understand correctly, the p-value is generated by comparing the in-frame and out-frame? I don't see any issue and I recommend to use weighted Fisher method in your case. Thanks.

Sora