diff --git a/tests/testthat/test-bulk_methods.R b/tests/testthat/test-bulk_methods.R index 3a32bb11..7343a083 100755 --- a/tests/testthat/test-bulk_methods.R +++ b/tests/testthat/test-bulk_methods.R @@ -84,7 +84,7 @@ test_that("Only scaled counts - no object",{ expect_equal( unique(res$multiplier), c(1.3078113, 1.1929933, 1.9014731, 0.9678922, 1.4771970), - tolerance=1e-3 + tolerance=1e-2 ) expect_equal( @@ -345,7 +345,7 @@ test_that("Only differential trancript abundance - no object",{ ) |> filter(FDR<0.05) |> nrow() |> - expect_equal(169) + expect_equal(171) }) @@ -603,7 +603,7 @@ test_that("Voom with treat method",{ res |> filter(`adj.P.Val___cell_typeb_cell-cell_typemonocyte` < 0.05) |> nrow() |> - expect_equal(293) + expect_equal(294) res |> filter(`adj.P.Val___cell_typeb_cell-cell_typet_cell`<0.05) |> @@ -695,7 +695,7 @@ test_that("DESeq2 differential trancript abundance - no object",{ expect_equal( unique(res$log2FoldChange)[1:4], c(3.449740, 2.459516, 2.433466, 1.951263), - tolerance=1e-3 + tolerance=1e-2 ) expect_equal( @@ -2007,7 +2007,7 @@ test_that("filter abundant with design - no object",{ ) |> filter(.abundant) |> nrow() |> - expect_equal(1965) + expect_equal(1970) diff --git a/tests/testthat/test-bulk_methods_SummarizedExperiment.R b/tests/testthat/test-bulk_methods_SummarizedExperiment.R index 3aae6428..3b9cd8b6 100755 --- a/tests/testthat/test-bulk_methods_SummarizedExperiment.R +++ b/tests/testthat/test-bulk_methods_SummarizedExperiment.R @@ -361,12 +361,14 @@ test_that("differential trancript abundance - SummarizedExperiment",{ as_tibble() |> filter(FDR<0.05) |> nrow() |> - expect_equal(169) + expect_equal(171) }) test_that("differential trancript abundance - SummarizedExperiment - alternative .abundance",{ + library(SummarizedExperiment) + assays(se_mini) = list(counts = assay(se_mini), bla = assay(se_mini)) @@ -440,7 +442,7 @@ test_that("differential trancript abundance - SummarizedExperiment - alternative as_tibble() |> filter(FDR<0.05) |> nrow() |> - expect_equal(169) + expect_equal(171) }) @@ -494,7 +496,7 @@ test_that("Voom with treat method",{ res |> filter(adj.P.Val___Cell.typeb_cell.Cell.typemonocyte < 0.05) |> nrow() |> - expect_equal(293) + expect_equal(294) res |> filter(adj.P.Val___Cell.typeb_cell.Cell.typet_cell < 0.05) |>