Different results if the dataset is used in intersect vs union join function
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venkat rami reddy
Mar 13, 2024, 11:30:57 AMMar 13
to TASSEL - Trait Analysis by Association, Evolution and Linkage
Hi all,
I am using an association panel in 147 bread wheat lines to conduct GWAS. I attempted both intersect and union joins for comparison, and after performing MLM, I observed that the Manhattan plots show differing results. The SNP significance varies.
Could there be a particular reason for this?
The genotype and phenotype files, as well as the PCA, all contain the same number of individuals and taxa names.
I am using an association panel in 147 bread wheat lines to conduct GWAS. I attempted both intersect and union joins for comparison, and after performing MLM, I observed that the Manhattan plots show differing results. The SNP significance varies.
Could there be a particular reason for this?
The genotype and phenotype files, as well as the PCA, all contain the same number of individuals and taxa names.
thanks in advance
Rami
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