Here are some common problems and their solutions.
This warning indicates that when optimizing the mu value for a guide, the log likelihood function returned NaN. This warning does not necessarily mean there is a problem.
There are three usual reasons for this:
1) Data that has really low coverage in the "input" and no pseudocount added (e.g. if A is 0% of the library, the likelihood of >1 reads in bin A is NaN)
To resolve the warning, please ensure that you are including a pseudocount to the data.
2) Data where one "guide" has really high abundance. (e.g. if a "guide" makes up 89% of your library, a Z score of 1 might mean that you now expect OVER 100% to end up in bin F)
Usually, MAUDE automatically restricting the search space will resolve this. The warning will stay, but you don't have to worry about it.
3) The mu search limits are too wide. (an extreme mu is so unlikely that the log likelihood is infinite, leading to this error)
If you only get this message a few times, there's no need to adjust anything; MAUDE automatically adjusts the search space. If many warnings are issued, it is recommended that you adjust the limits parameter. It defaults to c(-4,4). Adjusting it closer to 0 will eliminate the warning message.
Please submit an Issue, or contact the authors for any other problems you encounter so that we can fix/clarify things as necessary.