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To fit a model that has reps or any unbalanced design in BGLR, you need to first design the Z matrix, you can use model.matrix function for that. Then, in the ETA object you need to provide a ZGZ’ or ZM instead of standard X or K matrices. More on it here. Example below:
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Here, I show common genetic reasons where can lead to genomic relationship matrix (GRM) with problems in the inversion. They are commonly based on population structure or repeated (or highly similar) information. The cases are not always true, but they can represent why you have a strong linear dependence in your G matrix (Van Raden 2008) and a not unique inverse for the matrix. After identifying the reason, you can take action in order to manage the data before building the G matrix.
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Material developed for a workshop on R Parallel with Genomic Selection Application for the Genomic Selection Studies group at University of Florida, Gainesville, FL.
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Links to R tips and misc stuff
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For beginners with focus on Bioinformatics and Genetics
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The idea of this course is to introduce several cool graphics over different packages and how to build it step-by-step. Hopefully you will get some tools to run away from the basic R graphics.