update tests after limma's breaking changed calculation of degrees of…

… freedom (https://code.bioconductor.org/browse/limma/commit/e8ff47777e7c25d6dcb9582d9fcb8f9c4fed9da1)
fmicompbio · Aug 7, 2024 · 5b447f2 · 5b447f2
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: eisaR
 Title: Exon-Intron Split Analysis (EISA) in R
-Version: 1.17.0
+Version: 1.17.1
 Authors@R: c(person("Michael", "Stadler", email = "[email protected]", role = c("aut", "cre")),
              person("Dimos", "Gaidatzis", email = "[email protected]", role = "aut"),
              person("Lukas", "Burger", email = "[email protected]", role = "aut"),

diff --git a/tests/testthat/test_runEISA.R b/tests/testthat/test_runEISA.R
@@ -134,9 +134,10 @@ test_that("runEISA() gives expected results", {
                 test.sig = res2$tab.ExIn$FDR < 0.01) # close to 1/nsig -> one false positive
 
     # no false positives or false negatives (except for selsig2 genes in t1)
-    nmissed1 <- t1["TRUE", "TRUE", "FALSE"] # expect to miss some genes with sample-specific effects
+    nmissed1 <- t1["FALSE", "TRUE", "FALSE"] # these are now missed after updated df calculation in limma (https://code.bioconductor.org/browse/limma/commit/e8ff47777e7c25d6dcb9582d9fcb8f9c4fed9da1)
+    nmissed2 <- t1["TRUE", "TRUE", "FALSE"]  # expect to miss some genes with sample-specific effects
     expect_identical(as.vector(t1),
-                     c(ngenes - nsig, 0L, 0L, nmissed1, 0L, 0L, nsig - nsig2, nsig2 - nmissed1))
+                     c(ngenes - nsig, 0L, nmissed1, nmissed2, 0L, 0L, nsig - nsig2 - nmissed1, nsig2 - nmissed2))
     expect_identical(as.vector(t2),
                      c(ngenes - nsig, 0L, 0L, 0L, 0L, 0L, nsig - nsig2, nsig2))
 })