MutSigCV output has p-value of 0

Question

[varsha619]

Hi, I am running MutSigCV 1.0 using the public server and noticed that the top gene in my list of significantly mutated genes has a p-value of 0. I was wondering if I can get the exact p-value with decimals instead of rounded off to 0. Please advise.

Answer 1

[poisonAlien]

A p-value of 0 means the value is really low or close enough to zero. MutSig always produce 0 pvalue for overly significant genes such as TP53 in solid tumors. If you really want some value instead of zero, replace them with lowest machine epsilon values.

In r you could do this by

mutsig = read.delim('sig_genes.txt', sep = '\t', stringsAsFactors = FALSE, header = TRUE)
mach.epsi = .Machine$double.eps
mutsig$q = ifelse(test = mutsig$q == 0, yes = mach.epsi, no = mutsig$q)

[varsha619]

Got it, thank you so much!