The lme4 R package is a powerful tool for fitting mixed models in R where you can specify fixed and random effects. One oddity about the program is it returns t statistics, but no p-value. To get the p-value takes a little extra coding. Here is a quick example for fitting a linear mixed model in R (using lmer) and then the added code to calculate p-values from the t statistic. Either p1 or p2 are acceptable p-values to use.
Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.