diff --git a/R/ModuleScore.R b/R/ModuleScore.R
index b143f48f..466e9a4f 100644
--- a/R/ModuleScore.R
+++ b/R/ModuleScore.R
@@ -148,32 +148,46 @@ addModuleScore <- function(
     #Figure out the index numbers of the selected features within the given matrix
     if(grepl(":",unlist(features)[1])){
 
-      sname <- stringr::str_split(unlist(features),pattern=":",simplify=TRUE)[,1]
-      name <- stringr::str_split(unlist(features),pattern=":",simplify=TRUE)[,2]
-
-      idx <- lapply(seq_along(name), function(x){
-        ix <- intersect(
-          which(tolower(name[x]) == tolower(featureDF$name)), 
-          BiocGenerics::which(tolower(sname[x]) == tolower(featureDF$seqnames))
-        )
-        if(length(ix)==0){
-          .logStop(sprintf("FeatureName (%s) does not exist! See available features using getFeatures()", name[x]), logFile = logFile)
+      idx <- lapply(seq_along(features), function(x){
+        sname <- stringr::str_split(features[[x]], pattern=":", simplify=TRUE)[,1]
+        fname <- stringr::str_split(features[[x]], pattern=":", simplify=TRUE)[,2]
+
+        ix <- vapply(seq_along(fname), function(z){
+          hit <- intersect(
+            which(tolower(fname[z]) == tolower(featureDF$name)),
+            BiocGenerics::which(tolower(sname[z]) == tolower(featureDF$seqnames))
+          )
+          if(length(hit) == 0) return(NA_integer_)
+          hit[1]
+        }, integer(1))
+
+        missing <- features[[x]][is.na(ix)]
+        if(length(missing) > 0){
+          if(all(is.na(ix))){
+            .logStop(sprintf("All features (%s) in feature set %s not found! See available features using getFeatures()", paste(missing, collapse = ", "), x), logFile = logFile)
+          }
+          .logMessage(sprintf("Warning: %d of %d features not found and will be omitted: %s", length(missing), length(ix), paste(missing, collapse = ", ")), logFile = logFile)
+          warning(sprintf("Features not found and will be omitted: %s", paste(missing, collapse = ", ")))
+          ix <- ix[!is.na(ix)]
         }
         ix
       })
 
     }else{
 
-      idx <- lapply(seq_along(unlist(features)), function(x){
-      
-        ix <- which(tolower(unlist(features)[x]) == tolower(featureDF$name))[1]
-      
-        if(length(ix) == 0){
-          .logStop(sprintf("FeatureName (%s) no regions found overlapping! See available features using getFeatures()", unlist(features)[x]), logFile = logFile)
+      idx <- lapply(seq_along(features), function(x){
+
+        ix <- match(tolower(features[[x]]), tolower(featureDF$name))
+        missing <- features[[x]][is.na(ix)]
+        if(length(missing) > 0){
+          if(all(is.na(ix))){
+            .logStop(sprintf("All features (%s) in feature set %s not found! See available features using getFeatures()", paste(missing, collapse = ", "), x), logFile = logFile)
+          }
+          .logMessage(sprintf("Warning: %d of %d features not found and will be omitted: %s", length(missing), length(ix), paste(missing, collapse = ", ")), logFile = logFile)
+          warning(sprintf("Features not found and will be omitted: %s", paste(missing, collapse = ", ")))
+          ix <- ix[!is.na(ix)]
         }
-
         ix
-      
       })
 
     }
@@ -184,7 +198,7 @@ addModuleScore <- function(
       stop("Feature Input is Not A GRanges object!")
     }
 
-    idx <- lapply(seq_along(unlist(features)), function(x){
+    idx <- lapply(seq_along(features), function(x){
 
       #Check
       o <- tryCatch({GenomeInfoDb::seqlevelsStyle(features[[x]]) <- "UCSC"}, warning = function(w) 0, error = function(e) 0)
@@ -192,8 +206,8 @@ addModuleScore <- function(
       #Overlaps
       ix <- which(overlapsAny(featureData, features[[x]], ignore.strand=TRUE))
 
-      if(length(ix)==0){
-        .logStop(sprintf("FeatureName (%s) does not exist! See available features using getFeatures()", unlist(features)[x]), logFile = logFile)
+      if(length(ix) == 0){
+        .logStop(sprintf("All GRanges features in feature set %s have no overlapping regions! See available features using getFeatures()", x), logFile = logFile)
       }
       
       ix
diff --git a/R/RNAIntegration.R b/R/RNAIntegration.R
index 209aaa4d..8854a7b3 100644
--- a/R/RNAIntegration.R
+++ b/R/RNAIntegration.R
@@ -531,7 +531,7 @@ addGeneIntegrationMatrix <- function(
 
     if(addToArrow){
       .logDiffTime(sprintf("%s Seurat TransferData GeneMatrix", prefix), tstart, verbose = verbose, logFile = logFile)
-      transferParams$refdata <- GetAssayData(subRNA, assay = "RNA", slot = "data")
+      transferParams$refdata <- GetAssayData(subRNA, assay = "RNA", layer = "data")
       gc()
       matchedRNA <- do.call(Seurat::TransferData, transferParams)
       matchedRNA <- matchedRNA@data