Changing marker size for bonferoni correction

[mtross2]

Hi,

I'm calculated the number of effective SNPs and was wondering how I would be able to change marker size to this value so that I can have a corrected Bonferroni threshold according to the number of effective SNPs. How do I change that in rMVP? I tried doing threshold = 0.05/effective size but that seems to inflate the threshold value even more. Any suggestions would be appreciated!

[hyacz]

Thank you for using rMVP. Actually, the threshold is equal to -log10(threshold/n_marker). The number of markers will be automatically counted and used for Bonferroni correction. If you really want to modify it, you can set threshold = 0.05 * n_marker_old / n_marker_new.

[ramendra-sarma]

Thank you for using rMVP. Actually, the threshold is equal to -log10(threshold/n_marker). The number of markers will be automatically counted and used for Bonferroni correction. If you really want to modify it, you can set threshold = 0.05 * n_marker_old / n_marker_new.

What code shouls I use as " threshold = 0.05 * n_marker_old / n_marker_new" generate error