diff --git a/R/BulkProjection.R b/R/BulkProjection.R
index 882dd9a4..c60f4e10 100644
--- a/R/BulkProjection.R
+++ b/R/BulkProjection.R
@@ -81,7 +81,7 @@ projectBulkATAC <- function(
   # Create Bulk Matrix
   ##################################################
   bulkMat <- .safeSubset(
-    mat = .getAssay(subATAC, "counts"), 
+    mat = as.matrix(.getAssay(subATAC, "counts")), 
     subsetRows = paste0("f", seq_along(rDGR))
   )
   .logThis(bulkMat, "bulkATACMat", logFile = logFile)
@@ -145,13 +145,15 @@ projectBulkATAC <- function(
     if(!is.null(corCutOff)){
       if(scaleDims){
         corToDepth <- rD$corToDepth$scaled
-        dimsToUse <- dimsToUse[corToDepth < corCutOff]
+        dimsToUse <- dimsToUse[intersect(dimsToUse, which(corToDepth < corCutOff))]
       }else{
         corToDepth <- rD$corToDepth$none
-        dimsToUse <- dimsToUse[corToDepth < corCutOff]
+        dimsToUse <- dimsToUse[intersect(dimsToUse, which(corToDepth < corCutOff))]
       }
     }
 
+    simRD <- simRD[, dimsToUse, drop = FALSE]
+
     if(embedding$params$nc != ncol(simRD)){
       .logMessage("Error! Inconsistency found with matching LSI dimensions to those used in addUMAP or addTSNE",
         "\nReturning with simulated reduced dimension coordinates...", verbose = TRUE, logFile = logFile)
@@ -161,8 +163,6 @@ projectBulkATAC <- function(
       return(out)
     }
 
-    simRD <- simRD[, dimsToUse, drop = FALSE]
-
   }
 
   ##################################################
diff --git a/R/Embedding.R b/R/Embedding.R
index c71026f4..f32930b5 100644
--- a/R/Embedding.R
+++ b/R/Embedding.R
@@ -170,7 +170,7 @@ addUMAP <- function(
 
     ArchRProj@embeddings[[name]] <- SimpleList(
       df = dfEmbedding, 
-      params = c(
+      params = list(
         embeddingParams,
         dimsToUse = dimsToUse,
         scaleDims = scaleDims,
@@ -189,7 +189,7 @@ addUMAP <- function(
     embeddingParams$X <- NULL
     ArchRProj@embeddings[[name]] <- SimpleList(
       df = dfEmbedding, 
-      params = c(
+      params = list(
         embeddingParams,
         dimsToUse = dimsToUse,
         scaleDims = scaleDims,
diff --git a/R/HiddenUtils.R b/R/HiddenUtils.R
index 57fdad35..f5129b98 100644
--- a/R/HiddenUtils.R
+++ b/R/HiddenUtils.R
@@ -188,8 +188,18 @@
     idxNotIn <- which(subsetRows %ni% rownames(mat))
     if(length(idxNotIn) > 0){
       subsetNamesNotIn <- subsetRows[idxNotIn]
-      matNotIn <- Matrix::sparseMatrix(i=1,j=1,x=0,dims=c(length(idxNotIn), ncol = ncol(mat)))
+
+      #check matrix class and make a matching empty matrix for the idxNotIn rows
+      if (class(mat)[[1]] == "dgCMatrix") {
+        matNotIn <- Matrix::sparseMatrix(i = 1, j = 1, x = 0, dims = c(length(idxNotIn), ncol = ncol(mat)))
+      } else if (class(mat)[[1]] == "matrix") {
+        matNotIn <- matrix(nrow = length(idxNotIn), ncol = ncol(mat), 0)
+      } else{
+        stop("Error! Argument 'mat' in .safeSubset is not either of class matrix or class dgCMatrix!")
+      }
+      
       rownames(matNotIn) <- subsetNamesNotIn
+      colnames(matNotIn) <- colnames(mat)
       mat <- rbind(mat, matNotIn)
     }
     mat <- mat[subsetRows,]
@@ -199,7 +209,16 @@
     idxNotIn <- which(subsetCols %ni% colnames(mat))
     if(length(idxNotIn) > 0){
       subsetNamesNotIn <- subsetCols[idxNotIn]
-      matNotIn <- Matrix::sparseMatrix(i=1,j=1,x=0,dims=c(nrow(mat), ncol = length(idxNotIn)))
+
+      #check matrix class and make a matching empty matrix for the idxNotIn rows
+      if (class(mat)[[1]] == "dgCMatrix") {
+        matNotIn <- Matrix::sparseMatrix(i = 1, j = 1, x = 0, dims = c(nrow(mat), ncol = length(idxNotIn)))
+      } else if (class(mat)[[1]] == "matrix") {
+        matNotIn <- matrix(nrow = nrow(mat), ncol = length(idxNotIn), 0)
+      } else{
+        stop("Error! Argument 'mat' in .safeSubset is not either of class matrix or class dgCMatrix!")
+      }
+      rownames(matNotIn) <- rownames(mat)
       colnames(matNotIn) <- subsetNamesNotIn
       mat <- cbind(mat, matNotIn)
     }