I have performed GWAS analysis for disease resistance trait using 15000 DArT markers. How can I identify what markers are significant according to their P-values. I have read in few articles they consider values below 0.001 or 0.05 as significant. But is there any rule to decide what values are significant according to the number of markers or number of traits assessed?
would greatly appreciate if someone can explain this to me.
This decision based on number of Significant SNP/markers, Becuse if you get more number of MTAs, then you could increase your cutofff values even upto 0.000001 (10^-6). You can also use multiple testing correction (i.e. Bonferroini Correction). So it is upto you how much MTA associated, Suppose if at 0.01 you got 1000 MTAs then you can increase your significant level.
Hi Vijay,
Thank you for the info. Out of 15000 markers I am getting 9 markers below 0.001, does that mean I can increase my cut off value to such as 0.01?
I am only testing the markers association against one phenotypic trait i.e disease response.
I prefer to do it by FDR calculation! You can use the rrBLUP package!
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