Merge pull request #55 from StijnVandenbulcke/master

Newest bioconductor release
statOmics · Apr 22, 2024 · 6c2f36a · 6c2f36a
2 parents 308c1fd + b45cb96
commit 6c2f36a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: msqrob2
 Title: Robust statistical inference for quantitative LC-MS proteomics
-Version: 1.6.1
+Version: 1.11.1
 Authors@R: c(
       person(given = "Lieven",
            family = "Clement",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# msqrob 1.11.1
+
+- Fixed issues related to reference class changes in the models
+- Fixed issue related to colData assay levels
+- Refactored internal code
+
 # msqrob 1.6.2
 
 - Fixed issues related to residual degrees of freedom of overparameterized models.

diff --git a/R/msqrob-methods.R b/R/msqrob-methods.R
@@ -151,6 +151,8 @@ setMethod(
                 lmerArgs = lmerArgs
             )
         }
+
+        rowData(object)[[modelColumnName]] <- rowData(object)[[modelColumnName]][rownames(rowData(object))]
         return(object)
     }
 )
@@ -229,6 +231,8 @@ setMethod(
                 lmerArgs = lmerArgs
             )
         }
+
+        rowData(object[[i]])[[modelColumnName]] <- rowData(object[[i]])[[modelColumnName]][rownames(rowData(object[[i]]))]
         return(object)
     }
 )