You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I'm trying to run FDRreg with default parameters except for nulltype='empirical'. However, I get many warnings like the following:
f(z) misfit = -0.2. Rerun with increased df.
I think I have tracked this down to the efron function call. It seems to be an issue with the fitting of the empirical Z-score distribution. The warning suggests to run with an increased degrees of freedom, which is taken from the control input list (specifically, the densknots parameter, default value is 10). I tried to get advice for how much to increase this parameter from the documentation, but was a bit confused by the help file for FDRreg, which says:
nmids, densknots: Only used if method='efron'; this functionality is retained for legacy reasons and is not recommended for actual data analysis. nmids: How many histogram midpoints are used in Efron's spline-based estimator of f(z). Defaults to 150. densknots: how many spline knots. Defaults to 10.
Is the 'empirical' null type not recommended for actual data analysis? If it is, do you have any practical advice for how to set this densknots parameter?
Thanks in advance,
Keegan
The text was updated successfully, but these errors were encountered:
Thanks for bringing this up. You can use densknots with a higher value and it will behave as you expect, i.e. with a higher degrees of freedom for Efron's central matching estimator for the empirical null. It's the documentation that's deprecated rather than the function.
Hi,
I'm trying to run
FDRreg
with default parameters except for nulltype='empirical'. However, I get many warnings like the following:I think I have tracked this down to the
efron
function call. It seems to be an issue with the fitting of the empirical Z-score distribution. The warning suggests to run with an increased degrees of freedom, which is taken from thecontrol
input list (specifically, thedensknots
parameter, default value is 10). I tried to get advice for how much to increase this parameter from the documentation, but was a bit confused by the help file forFDRreg
, which says:Is the 'empirical' null type not recommended for actual data analysis? If it is, do you have any practical advice for how to set this
densknots
parameter?Thanks in advance,
Keegan
The text was updated successfully, but these errors were encountered: