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?
the first line of output will say LR test on 3 degrees of freedom, which is intended to alert you that the test is for all differences between the four treatments. You will also see multiple logFC columsn in the topTags table, one for each column of the contrast matrix, which again alerts you that the test is for multiple contrasts.
If on the other hand you test a single contrast, then the first line of output will tell you which contrast is being tested and there will be single logFC column in the topTags table.