I am using a function gammamixEM where it does it by default. I do not have the option to change it. Conceptually, what can make the algorithm not able to calculate likelihood value at all (and hence log-lik=Nan)? Is there sth wrong with the data? Under what conditions does it happen?
On Wed, Sep 14, 2016 at 8:04 PM, Duncan Murdoch <[email protected]> wrote: > On 14/09/2016 4:46 PM, Aanchal Sharma wrote: > >> Hi, >> >> I am trying to fit Gamma mixture model to my data (residual values >> obtained >> after fitting Generalized linear Model) using gammamixEM. It is part of >> the >> script which does it for multiple datasets in loop. The code is running >> fine for some datasets but it terminates for some giving following error: >> >> " iteration = 1 log-lik diff = NaN log-lik = NaN >> Error in while (diff > epsilon && iter < maxit) { : >> missing value where TRUE/FALSE needed" >> >> Seems like EM is not able to calculate log-lik value (NaN) at the first >> iteration itself. any idea why that can happen? >> It works fine for the other genes in the loop. Tried looking for >> difference >> in the inputs, but could not come up with anything striking. >> >> > THere are lots of ways to get NaN in numerical calculations. A common > one if you are using log() to calculate log likelihoods is that rounding > error gives you a negative likelihood, and then log(lik) comes out to NaN. > > You just need to look really closely at each step of your calculations. > Avoid using log(); use the functions that build it in (e.g. instead of > log(dnorm(x)), use dnorm(x, log = TRUE)). > > Duncan Murdoch > > -- Anchal Sharma, PhD Postdoctoral Fellow 195, Little Albany street, Cancer Institute of New Jersey Rutgers University NJ-08901 [[alternative HTML version deleted]] ______________________________________________ [email protected] mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
