Move computation of logcounts to ensure that tests work as expected.

pachterlab · Jul 22, 2024 · ad0e8ab · ad0e8ab
1 parent f2304d0
commit ad0e8ab
Showing 1 changed file with 2 additions and 3 deletions.
diff --git a/tests/testthat/test-concordex.R b/tests/testthat/test-concordex.R
@@ -4,10 +4,7 @@ library(TENxPBMCData)
 library(scater)
 
 sce <- TENxPBMCData("pbmc3k")
-
-# Make smaller
 sce <- sce[,seq(200)]
-sce <- logNormCounts(sce)
 
 sfe <- McKellarMuscleData("small")
 
@@ -31,6 +28,8 @@ test_that("concordex uses 'logcounts' by default for SCE objects", {
     )
 })
 
+sce <- logNormCounts(sce)
+
 test_that("Similarity matrix is not computed with continuous labels",{
     expect_warning(
         calculateConcordex(sce, "pca", compute_similarity=TRUE),