Question: Genome music,can P-value of smg be 0?
0
gravatar for Yuu
5.2 years ago by
Yuu10
China
Yuu10 wrote:

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!

 

smg genome music p-value • 1.5k views
ADD COMMENTlink modified 5.2 years ago by Chris Miller21k • written 5.2 years ago by Yuu10
1
gravatar for Chris Miller
5.2 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

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. 

ADD COMMENTlink written 5.2 years ago by Chris Miller21k

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?

ADD REPLYlink written 5.2 years ago by Yuu10

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.

ADD REPLYlink written 5.2 years ago by Philipp Bayer6.6k

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

ADD REPLYlink written 5.2 years ago by Yuu10
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