Effectively Identifying eQTLs from Multiple Tissues by Combining Mixed Model and Meta-analytic Approaches
This example has five samples (S1, S2, S3, S4, and S5) in three tissues (T1, T2, and T3). The leftmost table shows which tissues are collected from each sample; means gene expression of th sample in th tissue, and means the tissue is not collected. In this example, each tissue has gene expression measured in three samples. is a vector containing expression of samples in all tissues; there are a total of 9 gene expression values. In the matrix, denotes genotype of th sample. The matrix contains three intercepts () and three for the three tissues. is the random effect of the mixed model, and . is matrix whose entry at th row and th column is 1 if the th and th entries of are collected from the same individual, and 0 otherwise.