I have questions about the pvalues in the result from glmQLFTest.
For example, I have 4 treatments A, B, C, D, each has 3 replicates, and I want to compare any treatment pairs, i.e.: A-B, A-C, A-D, B-C, B-D, C-D. I use a matrix, generated by "makeContrasts" to define all the contrasts, then use "glmQLFTest" to test all the comparisons. In the resulting table, does the "PValue" refers to all the comparisons "logFC.A.B", "logFC.A.C", ..., "logFC.C.D" together as a whole? Or a specific comparison?