diff --git a/R/readWrite.R b/R/readWrite.R
index ed07e380..ee9dce71 100644
--- a/R/readWrite.R
+++ b/R/readWrite.R
@@ -42,7 +42,7 @@ writeBambuOutput <- function(se, path, prefix = "", outputExtendedAnno = TRUE,
         }
         #write incompatible counts
         if(!is.null(metadata(se)$incompatibleCounts)){
-            estimates = metadata(se)$incompatibleCounts
+            estimates <- metadata(se)$incompatibleCounts
             estimatesfn <- paste(transcript_gtffn, "incompatibleCounts.mtx", sep = "")
                 Matrix::writeMM(estimates, estimatesfn)
         }
diff --git a/R/transcriptToGeneExpression.R b/R/transcriptToGeneExpression.R
index 7ad12076..963a9b00 100644
--- a/R/transcriptToGeneExpression.R
+++ b/R/transcriptToGeneExpression.R
@@ -15,7 +15,7 @@ transcriptToGeneExpression <- function(se) {
     runnames <- colnames(counts)[-1]
     rowDataSe <- as.data.table(rowData(se))
     
-    counts  = fac2sparse(rowData(se)$GENEID) %*% counts
+    counts  = fac2sparse(factor(rowData(se)$GENEID, levels = unique(rowData(se)$GENEID))) %*% counts
     if(!is.null(metadata(se)$incompatibleCounts)){
         incompatibleCounts <- metadata(se)$incompatibleCounts
         if("nonuniqueCounts" %in% names(metadata(se))){