fix tests for new Bioconductor

stemangiola · Oct 16, 2024 · f62606a · f62606a
1 parent a0bdd3f
commit f62606a
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Showing 2 changed files with 10 additions and 8 deletions.
diff --git 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
@@ -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) |>