Tutorial questions #1
Description
Dear LFMM team.
I've been trying to use LFMM with my data, and for that I have tried to follow the tutorial you have provided.
Despite being rather complete, in the practical aspect, I am currently having some trouble with the interpretation.
My data is similar to that you present with A. thaliana, as it is a set of SNP markers where I am attempting to find associations with a set of environmental variables.
Here are my questions:
- When testing multiple environmental variables, should I correct the
calibrated.pvaluewith an FDR test? Or can the tests be considered independent between environmental variables? - When you show the p-values in a "Manhattan plot", you highlight some of the SNPs as "causal". I suppose you knew this a priori and thus, have such a list. If these were already known to be "causal" loci, how come so many of them are above the significance threshold? Is this expected?
Best regards,
Francisco
PS - Apologies if this is not the best channel to place these questions. In which case, could you please point me towards the preferred method of asking them.