tests/testthat/test_factors.R

In DESeq2: Differential gene expression analysis based on the negative binomial distribution

context("factors")
test_that("bad factor in design throw errors", {
  dds <- makeExampleDESeqDataSet(n=100, m=6)
  levels(dds$condition) <- c("test-","test+")
  expect_error(DESeq(dds))

  dds <- makeExampleDESeqDataSet(n=100, m=6)
  dds$condition <- factor(rep(letters[1:3], each=2), ordered=TRUE)
  expect_error(DESeq(dds))
  mm <- model.matrix(~ condition, data=colData(dds))
  dds <- DESeq(dds, full=mm) # betaPrior=FALSE
})