diff --git a/tools/edger/edger.R b/tools/edger/edger.R
index 0d8be1d901b..1b0fdc96db9 100644
--- a/tools/edger/edger.R
+++ b/tools/edger/edger.R
@@ -283,7 +283,7 @@ if (!is.null(opt$filesPath)) {
     }
     # order samples as in counts matrix
     factordata <- factordata[match(colnames(counts), factordata[, 1]), ]
-    factors <- factordata[, -1, drop = FALSE]
+    factors <- data.frame(sapply(factordata[, -1, drop = FALSE], make.names))
   } else {
     factors <- unlist(strsplit(opt$factInput, "|", fixed = TRUE))
     factordata <- list()
diff --git a/tools/edger/edger.xml b/tools/edger/edger.xml
index 137a599d688..ee7cad7e6b3 100644
--- a/tools/edger/edger.xml
+++ b/tools/edger/edger.xml
@@ -4,7 +4,7 @@
     </description>
     <macros>
         <token name="@TOOL_VERSION@">3.36.0</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <edam_topics>
         <edam_topic>topic_3308</edam_topic>