p-value of being somatic using Fisher's test

[skiguy]

Hi,

I was wondering if someone can give an explanation of exactly what this is testing and why it is needed? I have received a data set with this but am not quite sure exactly what the null vs alternative is? Shouldn't it be known whether the mutation is somatic (I'm assuming as compared to germline)?

Thanks for the help!

[sdavis]

Take a look at http://seqanswers.com/forums/showthread.php?t=17079.

[skiguy]

Hi,

Thanks for that, it was very helpful. In my file, I have a whole list of FET values for about 25,000 mutations. So if I wanted to use only the somatic ones (with a cut of 5%) would I have to do some sort of Bonferroni adjustment or something similar?

Thanks again!