@@ -1014,23 +1014,17 @@ addLogLikelihood <- function(llA, llB) {

   }

   sce <- scater::logNormCounts(sce, log = TRUE)

-  if (nrow(sce) <= varGenes) {

-    topVariableGenes <- seq_len(nrow(sce))

-  } else if (nrow(sce) > varGenes) {

-    sce.var <- scran::modelGeneVar(sce)

-    topVariableGenes <- order(sce.var$bio,

-      decreasing = TRUE

-    )[seq(varGenes)]

-  }

-  sce <- sce[topVariableGenes, ]

-

   if (!is.null(seed)) {

     with_seed(

       seed,

-      resUmap <- scater::calculateUMAP(sce, n_threads = 1)

+      resUmap <- scater::calculateUMAP(sce, ntop = varGenes,

+                                       n_threads = 1,

+                                       exprs_values = "logcounts")

     )

   } else {

-    resUmap <- scater::calculateUMAP(sce, n_threads = 1)

+    resUmap <- scater::calculateUMAP(sce, ntop = varGenes,

+                                     n_threads = 1,

+                                     exprs_values = "logcounts")

   }

   z <- NULL