If there are unequal number of genotypes per site to be evaluated thean what could be best software to find GXE interaction i.e.I have 10 sites but in each site number of genotypes varies from 3 to 8. How it can be analyses
Sharing link:
https://link.springer.com/article/10.1007/s11295-016-1081-0
Regards!
Hope it will be useful
Regards
If there are known relationships between your genotypes, you can use a relationship matrix to account for uneven replication.
Attached is another paper where we use very unbalanced data over years and sites, with pedigree information, and adjustments for spatial variation.
Genome 53:992, Beeck et al. 2010
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