diff --git a/R/branchPropTest.R b/R/branchPropTest.R
index 8a48631..a4dcc91 100644
--- a/R/branchPropTest.R
+++ b/R/branchPropTest.R
@@ -15,7 +15,7 @@ branchPropTest <- function(data, design, method = 't.test') {
   if (method == 't.test'){
     id1 = which(design[, 2] == 0)
     id2 = which(design[, 2] == 1)
-    res <- apply(data, 1, function(i)
+    res <- apply(data[,design[,1]], 1, function(i)
       t.test(i[id1], i[id2])$p.value)
     
   }
diff --git a/R/cellPropTest.R b/R/cellPropTest.R
index e9e74f4..60f594c 100644
--- a/R/cellPropTest.R
+++ b/R/cellPropTest.R
@@ -21,6 +21,7 @@ cellPropTest <- function(cellanno,
                          design = NULL,
                          ncores = detectCores(),
                          test.type = 'variable',
+                         permuiter = 100,
                          testvar = 2) {
   ptw <-
     cut(pseudotime, seq(min(pseudotime), max(pseudotime), length.out = 100), include.lowest = T)
@@ -54,6 +55,7 @@ cellPropTest <- function(cellanno,
       ncores = ncores,
       test.type = test.type,
       test.method = 'permutation',
+      permuiter = permuiter,
       ncores.fit = 1,
       fix.all.zero = F
     )
diff --git a/R/getPopulationFit.R b/R/getPopulationFit.R
index da10f4d..5dc26d9 100644
--- a/R/getPopulationFit.R
+++ b/R/getPopulationFit.R
@@ -17,7 +17,7 @@
 getPopulationFit <- function(testobj,
                              gene = NULL,
                              type = 'time',
-                             num.timepoint = 1e3){
+                             num.timepoint = max(testobj$pseudotime)){
   type <- toupper(type)
   if (!'testvar' %in% names(testobj)) {
     testvar <- testobj$testvar <- 2