why Hardy-Weinberg test is different in GenABEL and Plink?

Question

When I use this Plink command:

Plink --file filename --hardy

will create a new file filename.hwe with the different p-value for each marker, by contrast with GenABEL :

library(GenABEL)
...
snpSummary<-summary(gtdata(filename))
hwe_test<-snpSummary$Pexact

Why do I get other p-values for the same markers?

It would help very much if you gave us some sample data, and then show exactly how the results differ between the two. Also put a `library()` statement at the top of your `R` code so we know what packages you are using, and we can just cut and paste it into our browsers. — nograpes, Apr 11 '13 at 17:28

score 2 · Answer 1 · answered Apr 11 '13 at 17:42

2

There are different tests of HWE. For instance chi square goodness of fit vs Fishers exact tests vs heterozygote excess/deficit.

I don't know for sure, but you should check the manual of each software to confirm they're using identical tests first.

answered Apr 11 '13 at 17:42

KKeenan

Thank you KKeenan, the software don't provide any information about what you say! only commands to execute. – Hocine Ben Apr 12 '13 at 16:22

1 Answers1