Hi
I want to run a statistical test to identify gene families (GFs) with a significant expansion/loss of genes between three species (A,B and C).
For each species I have the number of genes for each gene family:
A B C TOTAL
GF_1 50 50 50 150
GF_2 100 20 50 170
GF_3 7 2 1 10
GF_X ....
I searched in the available literature, and either Fisher, Chi-squared or a binomial test are proposed, but I can not find which one is the best to apply on my data?
Any help is much appreciated.
We usually use fisher exact test to detect the expansion and contraction of gene families. But for phylogenomics analysis, l prefer using CAFE.
Again, what does a p-value even tell you in this context? Unless there's heterogeneity within the population a change in family size of any amount always constitutes a change. There's no additional coherent concept of significance that can be attached to that.
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Why do you need to assign a p-value to this? I don't think that makes any sense in this context (unless there's heterogeneity within members of each species...but that would vary by gene family).