@@ -166,7 +166,8 @@ evaluateDimRed <- function(x, clusters=NULL, n=c(10,20,50), covars){

     x <- Embeddings(x[["pca"]])

   }else if(is(x, "SingleCellExperiment")){

     if(is.character(covars))

-      covars <- as.data.frame(colData(x)[,intersect(covars,colnames(colData(x))])

+      covars <- as.data.frame(colData(x)[,

+                                    intersect(covars,colnames(colData(x)))])

     if(is.null(clusters)) clusters <- x$phenoid

     x <- reducedDim(x, "PCA")

   }else{