diff --git a/R/analysis.R b/R/analysis.R
index ee02b79..77583bb 100644
--- a/R/analysis.R
+++ b/R/analysis.R
@@ -49,7 +49,7 @@ netAnalysis_contribution <- function(object, signaling, signaling.name = NULL, w
     pairLR <- pairLR[pairLR.name.use,]
   }
 
-  prob <- prob[,,pairLR.name.use]
+  prob <- prob[,,pairLR.name.use, drop=FALSE]
 
   if (length(dim(prob)) == 2) {
     prob <- replicate(1, prob, simplify="array")
@@ -981,7 +981,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
         }
       }
       idx.t <- setdiff(1:nrow(prob), sources.use)
-      prob[idx.t, , ] <- 0
+      prob[idx.t, , ,drop=FALSE] <- 0
     }
     if (!is.null(targets.use)) {
       if (is.character(targets.use)) {
@@ -992,7 +992,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
         }
       }
       idx.t <- setdiff(1:nrow(prob), targets.use)
-      prob[ ,idx.t, ] <- 0
+      prob[ ,idx.t, ,drop=FALSE] <- 0
     }
     if (sum(prob) == 0) {
       stop("No inferred communications for the input!")
@@ -1058,7 +1058,7 @@ rankNet <- function(object, slot.name = "netP", mode = c("comparison", "single")
           }
         }
         idx.t <- setdiff(1:nrow(prob), targets.use)
-        prob[ ,idx.t, ] <- 0
+        prob[ ,idx.t, , drop=FALSE] <- 0
       }
       if (sum(prob) == 0) {
         stop("No inferred communications for the input!")
diff --git a/R/modeling.R b/R/modeling.R
index 2db536d..fad8c70 100644
--- a/R/modeling.R
+++ b/R/modeling.R
@@ -375,10 +375,10 @@ computeCommunProbPathway <- function(object = NULL, net = NULL, pairLR.use = NUL
   group <- factor(pairLR.use$pathway_name, levels = pathways)
   prob.pathways <- aperm(apply(prob, c(1, 2), by, group, sum), c(2, 3, 1))
   pathways.sig <- pathways[apply(prob.pathways, 3, sum) != 0]
-  prob.pathways.sig <- prob.pathways[,,pathways.sig]
+  prob.pathways.sig <- prob.pathways[,,pathways.sig, drop=FALSE]
   idx <- sort(apply(prob.pathways.sig, 3, sum), decreasing=TRUE, index.return = TRUE)$ix
   pathways.sig <- pathways.sig[idx]
-  prob.pathways.sig <- prob.pathways.sig[, , idx]
+  prob.pathways.sig <- prob.pathways.sig[, , idx, drop=FALSE]
 
   if (is.null(object)) {
     netP = list(pathways = pathways.sig, prob = prob.pathways.sig)