In the last block of code in the edgeR script there is a mistake. In order to generate a vector of logical values that corresponds to the significant genes, you will need to run the following code instead of what is currently in the script :


# Get significant genes
sigKD <- decideTestsDGE(lrt_kd, adjust.method="BH", p.value = 0.01)
sigKD <- as.logical(abs(sigKD) > 0)

sigOE <- decideTestsDGE(lrt_oe, adjust.method="BH", p.value = 0.01)
sigOE <- as.logical(abs(sigOE) > 0)
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