Fix FindMarkers for SCT

wicky-dot · Nov 7, 2022 · 755a6bf · 755a6bf
1 parent 691e31a
commit 755a6bf
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Showing 2 changed files with 6 additions and 5 deletions.
diff --git a/R/differential_expression.R b/R/differential_expression.R
@@ -761,8 +761,9 @@ FindMarkers.SCTAssay <- function(
     pseudocount.use = pseudocount.use,
     mean.fxn = mean.fxn,
     fc.name = fc.name,
-    base = base
-  )
+    base = base,
+    norm.method = 'LogNormalize' # do expm1 on data slot
+    )
   de.results <- FindMarkers(
     object = data.use,
     slot = data.slot,
@@ -784,7 +785,7 @@ FindMarkers.SCTAssay <- function(
     pseudocount.use = pseudocount.use,
     fc.results = fc.results,
     densify = densify,
-    norm.method = 'LogNormalize' # do expm1 on data slot
+    norm.method = 'LogNormalize', # do expm1 on data slot
     ...
   )
   return(de.results)

diff --git a/tests/testthat/test_differential_expression.R b/tests/testthat/test_differential_expression.R
@@ -46,11 +46,11 @@ test_that("Default settings work as expected", {
 
   # SCT normalization
   expect_equal(results.sct[1, "p_val"], 6.225491e-11)
-  expect_equal(results.sct[1, "avg_logFC"], -0.6768721, tolerance = 1e-6)
+  expect_equal(results.sct[1, "avg_logFC"], -1.081321, tolerance = 1e-6)
   expect_equal(results.sct[1, "pct.1"], 0.111)
   expect_equal(results.sct[1, "pct.2"], 0.96)
   expect_equal(results.sct[1, "p_val_adj"], 1.369608e-08)
-  expect_equal(nrow(x = results.sct), 92)
+  expect_equal(nrow(x = results.sct), 158)
   expect_equal(rownames(x = results.sct)[1], "TYMP")
 })