Genome music,can P-value of smg be 0?
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Entering edit mode
6.9 years ago
Yuu ▴ 10

Hi, I am new to Music and there was a question bothered me.

I use music to find significant mutation gene，and the result shows that there are some genes' P-value are 0.How can the P-value be 0?

Here are the code and part of my output.

code:

genome music smg \
--gene-mr-file gene_coverage/gene_mrs \
--output-file Music_smg.out.xls

output:

 Muts pMbp P-value FCPT P-value LRT P-value CT FDR FCPT FDR LRT FDR CT 248.8 0 0 0 0 0 0 72.84 0 0 0 0 0 0 109.8 1.99E-14 0 5.66E-21 1.56E-10 0 4.45E-17 16483.52 6.22E-11 9.10E-15 5.40E-15 3.67E-07 3.58E-11 3.19E-11 11.49 2.86E-10 0 1.02E-14 1.35E-06 0 4.81E-11 37.2 3.22E-09 3.61E-13 7.42E-14 1.27E-05 8.64E-10 2.92E-10 93.68 2.38E-08 7.44E-15 2.07E-13 8.03E-05 3.51E-11 6.97E-10 117.15 3.51E-08 4.20E-12 4.54E-13 0.000103511 7.62E-09 1.34E-09

Thank you very much for your help!

Genome music smg P-value • 1.8k views
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Entering edit mode
6.9 years ago

This generally means the p-value is below the level that can be represented by the numeric storage type. You're right that it's not exactly zero, but it gets rounded to zero when sufficiently small.

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Thank you very much for your answer，and I still have a question,is there a cutoff that “below the level that can be represented by the numeric storage type” in Music?

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I may be wrong:

in MuSiC's code from http://apt.genome.wustl.edu/ubuntu/pool/main/g/genome-music/genome-music_0.4.1-1.tar.gz in the file "ClinicalCorrelation.pm" there is a comment that says:

>Internally, the input data is fed into an R script which calculates a P-value representing the
probability that the correlation seen between the mutations in each gene (or variant) and each
phenotype trait are random. Lower P-values indicate lower randomness, or likely true correlations.

So the lowest p-value depends on your R installation.

In R, when you run the command  .Machine\$double.xmin you get the lowest possible floating value on your machine, which in my case is 2.225074e-308, tiny! It may vary on your machine, especially if it's still a 32 bit machine.

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It helps a lot,i found the similar description in Smg.pm，thks very much！