Frequently Asked Questions

We will continue to update this list to address the more common questions.

1. I've receive the following error message, what should I do?

   GLM model did not converge! Please send me the DEBUG files

   This error message means that the logistic regression model cannot converge. This is usually caused by small sample size or caused by problem in the input file.

   You should first check the DEBUG file and see if that contains any NaN or Inf. These will likely be caused by un-quality controlled input, which can contain complete missingness. If that isn't the case, then you can load the DEBUG and DEBUG.y file into R and see if you can perform the logistic regression on the data (DEBUG.y is the y, whereas DEBUG contains the independent variables, including the intercept).

2. My base/ target data do not contain the RS ID. Can I still use PRSice?

   As of version 2.3.x, PRSice now support chromosome ID via the parameter --chr-id. --chr-id will automatically generate an ID for each of your SNPs based on user input string, some characters are reserved:

   c = chromosome
   l = coordinates
   a = effective allele
   b = non-effective allele
   

   So --chr-id c:l-ab will construct SNP ID as <chromosome>:<coordinate>-<effective allele><non-effective allele>

   Note

   It is not case sensitive