test_that("DESeq() gives correct errors", {
  dds <- makeExampleDESeqDataSet(n=100, m=8)
  expect_error(DESeq(dds, test="LRT"))
  expect_error(DESeq(dds, test="Wald", full=~condition, reduced=~1))
  expect_error(DESeq(dds, full=~1))
  m <- model.matrix(~ condition, colData(dds))
  expect_error(DESeq(dds, test="LRT", full=m, reduced=~1))
  expect_error(DESeq(dds, test="LRT", full=m, reduced=m))
  expect_error(DESeq(dds, full=m, betaPrior=TRUE))
  design(dds) <- ~ 0 + condition
  expect_error(DESeq(dds, betaPrior=TRUE))
  dds <- makeExampleDESeqDataSet(n=100)
  dds$condition <- factor(rep(c("A","B","C"),each=4))
  dds <- dds[,1:8]

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DESeq2 documentation built on Feb. 22, 2021, 10 a.m.