MadsonBrowning Pvalue is zero

[zx8754]

MadsonBrowning test results have zero values for "PermPvalue", does this mean Pvalue is so small that it is rounded to 0 and we should consider it as "significant", or this Pvalue is supposed to be NA?

Here is subset of example output, see gene2:

Gene    RANGE   N_INFORMATIVE   NumVar  NumPolyVar  NumPerm ActualPerm  Stat    NumGreater  NumEqual    PermPvalue
gene1   x   x   3   3   10000   10000   4.79095 672 0   0.0672
gene2   x   x   1   1   10000   10000   1.19513 0   0   0
gene3   x   x   3   3   10000   1000    4.28E-06    1000    0   1

[zx8754]

Here is a better example, where all tests give "significant" pvalue, while MB is zero:

#skatO                          
Range   RANGE   N_INFORMATIVE   NumVar  NumPolyVar  Q   rho Pvalue
geneX   x   x   11  11  58761.7 1   0.000204181

#MadsonBrowning                                     
Range   RANGE   N_INFORMATIVE   NumVar  NumPolyVar  NumPerm ActualPerm  Stat    NumGreater  NumEqual    PermPvalue
geneX   x   x   11  11  10000   10000   16.6566 0   0   0

#CMC                        
Range   RANGE   N_INFORMATIVE   NumVar  NumPolyVar  NonRefSite  Pvalue
geneX   x   x   11  11  22  0.000121977

#Zeggini                    
Range   RANGE   N_INFORMATIVE   NumVar  NumPolyVar  Pvalue
geneX   x   x   11  11  0.000204544

[zhanxw]

The permutation p-value is exactly zero, and it is calculated based on 10,000 permutations. I think if the number of permutation increases, you will get non-zero p-values for MadsonBrowning test.

[zx8754]

I see, this answers my question then, zero means value is very close to zero and is significant. Thank you.