Genome Music: Most significant hits lack p-value

Question

[Chirag Nepal]

Hi there,

I used genome MuSiC to measure the significance of mutated genes. Everything works fine, but the most significant hits do not have p-value, as it is simply written as "0".

For eg: Gene Indels SNVs Tot Muts Covd Bps Muts pMbp P-value FCPT P-value LRT P-value CT FDR FCPT FDR LRT FDR CT

TP53 0 17 17 20372 834.48 0 0 0 0 0 0

BAP1 3 3 6 32323 185.63 2.88295257655502e-06 1.00335850738986e-10 3.54967231991123e-10 0.030926873764994 1.07635283880247e-06 3.80791098118477e-06

CDC27 0 4 4 40136 99.66 0.000138356655441818 1.08419471067656e-07 4.851087615328e-08 0.989480680834735 0.00058153493793914 0.000346933615956207

Any suggestions on how to extract the p-value to plot. thanks !

Answer 1

[Chris Miller]

You're limited by the ability of your system/language to support very small floating point numbers. At some point, it just throws up it's hands and says "it's essentially zero".

[Chirag Nepal]

That is what i thought. Do you have any suggestions on how to extract those p-values, in case of genome MuSic.

For eg: in R, p-value < 2E16 are generally given 0, but there is way to get the p-value. So wondering if i can do same thing in Music.

[Chris Miller]

Sorry, I don't know that.