diff --git a/NAMESPACE b/NAMESPACE
index 777fa855..7e7e018c 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -72,6 +72,8 @@ importFrom(graphics,barplot)
 importFrom(graphics,par)
 importFrom(methods,as)
 importFrom(methods,is)
+importFrom(methods,setGeneric)
+importFrom(methods,setMethod)
 importFrom(parallel,mclapply)
 importFrom(rlang,.data)
 importFrom(stats,cor)
diff --git a/R/fixCompartments.R b/R/fixCompartments.R
index 8485a952..867ff354 100644
--- a/R/fixCompartments.R
+++ b/R/fixCompartments.R
@@ -2,7 +2,7 @@
 #'
 #' @name fixCompartments
 #'
-#' @param obj Input RaggedExperiment or output of condenseSE
+#' @param x Input RaggedExperiment or output of condenseSE
 #' @param min.conf Minimum confidence score to use
 #' @param parallel Whether to run in parallel
 #' @param cores How many cores to use if running in parallel
@@ -10,24 +10,28 @@
 #' @return A "fixed" set of compartments
 #' @import RaggedExperiment
 #' @import SummarizedExperiment
+#' @importFrom methods setGeneric setMethod standardGeneric
 #' @export
 #'
 #' @examples
-fixCompartments <- function(obj, min.conf = 0.8, parallel = FALSE, cores = 1) {
-  # this function will invert or "fix" compartments based on bootstrapping results
-  if (is(obj, "RaggedExperiment")) obj <- condenseSE(obj, sample.name = colnames(assay(obj)))
+setGeneric("fixCompartments", function(x, min.conf = 0.8, parallel = FALSE, cores = 1) {
+  standardGeneric("fixCompartments")
+})
 
-  # if we somehow only have 1 sample
-  if (is(obj, "GRanges")) {
-    return(flipper(obj, min.conf))
-  }
+setMethod("fixCompartments", "GRanges", function(x, min.conf = 0.8, parallel = FALSE, cores = 1) {
+  message("Assuming we only have a single sample to process")
+  message("Fixing compartments using a minimum confidence score of ", min.conf * 100, "%")
+  flipper(x, min.conf)
+})
 
+setMethod("fixCompartments", "RaggedExperiment", function(x, min.conf = 0.8, parallel = FALSE, cores = 1) {
+  obj <- condenseSE(x, sample.name = colnames(assay(x)))
   message("Fixing compartments using a minimum confidence score of ", min.conf * 100, "%")
   # go through and invert compartments based on the min.conf
   flip_compartments_lst <- mclapply(obj, flipper, min.conf, mc.cores = ifelse(parallel, cores, 1))
   names(flip_compartments_lst) <- names(obj)
-  return(flip_compartments_lst)
-}
+  RaggedExperiment(flip_compartments_lst)
+})
 
 #' Helper to invert, or "fix", compartments that have a minimum confidence score (1-min.conf)
 #'
@@ -41,8 +45,6 @@ flipper <- function(input_obj, min.conf) {
     stop("Bootstrapping was not performed. Cannot fix compartments.")
   }
 
-  message("Assuming we only have a single sample to process.")
-  message("Fixing compartments using a minimum confidence score of ", min.conf * 100, "%")
   invert_compartments <- apply(mcols(input_obj), 1, .inverter, min.conf)
   mcols(input_obj)$flip.compartment <- invert_compartments
 
diff --git a/man/fixCompartments.Rd b/man/fixCompartments.Rd
index abaaf6e2..71d322f6 100644
--- a/man/fixCompartments.Rd
+++ b/man/fixCompartments.Rd
@@ -4,10 +4,10 @@
 \alias{fixCompartments}
 \title{Invert, or "fix", compartments that have a minimum confidence score (1-min.conf)}
 \usage{
-fixCompartments(obj, min.conf = 0.8, parallel = FALSE, cores = 1)
+fixCompartments(x, min.conf = 0.8, parallel = FALSE, cores = 1)
 }
 \arguments{
-\item{obj}{Input RaggedExperiment or output of condenseSE}
+\item{x}{Input RaggedExperiment or output of condenseSE}
 
 \item{min.conf}{Minimum confidence score to use}
 
diff --git a/tests/testthat/test-fixCompartments.R b/tests/testthat/test-fixCompartments.R
index e4b7cc28..f647a331 100644
--- a/tests/testthat/test-fixCompartments.R
+++ b/tests/testthat/test-fixCompartments.R
@@ -90,6 +90,6 @@ test_that("fixCompartments", {
   re <- RaggedExperiment(A = gr1, B = gr2, C = gr3)
   fix_result <- fixCompartments(re)
 
-  expect_length(fix_result, length(colnames(re)))
-  expect_equal(names(fix_result), c("A", "B", "C"))
+  expect_equal(ncol(fix_result), ncol(re))
+  expect_equal(colnames(fix_result), c("A", "B", "C"))
 })
diff --git a/vignettes/compartmap.Rmd b/vignettes/compartmap.Rmd
index 86324010..3d805f05 100644
--- a/vignettes/compartmap.Rmd
+++ b/vignettes/compartmap.Rmd
@@ -87,7 +87,8 @@ k562_compartments.boot.fix <- fixCompartments(
 )
 
 # Look at the first cell in the GRangesList object
-k562_compartments.boot.fix[[1]]
+k562_compartments.grlist <- condenseSE(k562_compartments.boot.fix)
+k562_compartments.grlist[[1]]
 ```
 
 ### Visualization of inferred chromatin domains
@@ -107,7 +108,7 @@ intervals and median confidence estimate:
 
 ```{r postprocessPlot, warning=FALSE}
 plotAB(
-  k562_compartments.boot.fix[[1]],
+  k562_compartments.grlist[[1]],
   chr = "chr14",
   with.ci = TRUE,
   median.conf = TRUE
@@ -140,7 +141,7 @@ extract single-cell domain inflections:
 
 ```{r postprocessInflections, message=FALSE, warning=FALSE}
 k562_cell_1_inflections <- getDomainInflections(
-  k562_compartments.boot.fix[[1]],
+  k562_compartments.grlist[[1]],
   what = "flip.score",
   res = 1e6,
   chrs = "chr14",