diff --git a/DESCRIPTION b/DESCRIPTION
index 21e138e..a04a3fa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: CAGEr
 Title: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
-Version: 2.11.3
-Date: 2024-05-24
+Version: 2.11.4
+Date: 2024-08-02
 Authors@R:
   c( person("Vanja",   "Haberle",   email = "vanja.haberle@gmail.com",       role = "aut"),
      person("Charles", "Plessy",    email = "charles.plessy@oist.jp",        role = "cre"),
diff --git a/NAMESPACE b/NAMESPACE
index d835e37..1e9f865 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -40,6 +40,7 @@ export(distclu)
 export(exportToTrack)
 export(expressionClasses)
 export(filterLowExpCTSS)
+export(filteredCTSSidx)
 export(findStrandInvaders)
 export(flagByUpstreamSequences)
 export(flagLowExpCTSS)
diff --git a/NEWS.md b/NEWS.md
index 600c000..b675b95 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# Upcoming changes in version 2.11.4
+# Changes in version 2.11.4
 
 BACKWARDS-INCOMPATIBLE CHANGES
 
@@ -8,6 +8,11 @@ NEW FEATURES
 
 -   Support the use of `TxDB` objects for annotating clusters.
 
+BUG FIXES
+
+-   Fix issue #120 introduced in 2.11.3, where clustering functions would
+    fail if `filterLowExpCTSS` was not run before.
+
 # Changes in version 2.11.3
 
 BACKWARDS-INCOMPATIBLE CHANGES
diff --git a/R/CAGEr.R b/R/CAGEr.R
index f914572..388913b 100644
--- a/R/CAGEr.R
+++ b/R/CAGEr.R
@@ -182,6 +182,8 @@ setMethod("validSamples", "CAGEr", function (object, x){
 #' 
 #' @export
 #' 
+#' @family CAGEr filter functions
+#' 
 #' @examples
 #' flagLowExpCTSS(exampleCAGEexp, threshold = 100, nrPassThreshold = 2)
 
diff --git a/R/GetMethods.R b/R/GetMethods.R
index c00b832..c7c78a5 100644
--- a/R/GetMethods.R
+++ b/R/GetMethods.R
@@ -454,13 +454,32 @@ setMethod( "tagClustersGR", "CAGEexp"
   .TagClusters(tc)
 })
 
-#' @name filteredCTSSidx
-#' @noRd
+#' The `filteredCTSSidx()` function is in _CAGEr_ functions to retrieve the
+#' result of the `flagLowExpCTSS()` function in a safe way.
+#' 
+#' @returns Returns the value of `filteredCTSSidx` in the row ranges of the
+#' tag count matrix experiment of the `CAGEexp` object, or `Rle(TRUE)` if it
+#' was `NULL`
+#' 
+#' @param object A [`CAGEexp`] object
+#' 
+#' @export
+#' 
+#' @examples
+#' 
+#' filteredCTSSidx(exampleCAGEexp)
+#' 
+#' @family CAGEr filter functions
+#' @family CAGEr accessor methods
 
 setGeneric("filteredCTSSidx", function(object) standardGeneric("filteredCTSSidx"))
 
+#' @rdname filteredCTSSidx
+
 setMethod("filteredCTSSidx", "CAGEexp", function (object){
-  rowData(CTSStagCountSE(object))$filteredCTSSidx
+  res <- rowData(CTSStagCountSE(object))$filteredCTSSidx
+  if (is.null(res)) return(Rle(TRUE))
+  res
 })
 
 
diff --git a/man/CTSScoordinates.Rd b/man/CTSScoordinates.Rd
index 2d2710d..ce3cea7 100644
--- a/man/CTSScoordinates.Rd
+++ b/man/CTSScoordinates.Rd
@@ -52,6 +52,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/CTSScumulativesTagClusters.Rd b/man/CTSScumulativesTagClusters.Rd
index f54b4c0..1894baf 100644
--- a/man/CTSScumulativesTagClusters.Rd
+++ b/man/CTSScumulativesTagClusters.Rd
@@ -55,6 +55,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/CTSSnormalizedTpm.Rd b/man/CTSSnormalizedTpm.Rd
index 6da6318..392b1f8 100644
--- a/man/CTSSnormalizedTpm.Rd
+++ b/man/CTSSnormalizedTpm.Rd
@@ -46,6 +46,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/CTSStagCount.Rd b/man/CTSStagCount.Rd
index 8d16071..1718d0e 100644
--- a/man/CTSStagCount.Rd
+++ b/man/CTSStagCount.Rd
@@ -63,6 +63,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/GeneExpDESeq2.Rd b/man/GeneExpDESeq2.Rd
index a31e2fd..0c59f4f 100644
--- a/man/GeneExpDESeq2.Rd
+++ b/man/GeneExpDESeq2.Rd
@@ -40,6 +40,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/GeneExpSE.Rd b/man/GeneExpSE.Rd
index 5445e1b..7ad4176 100644
--- a/man/GeneExpSE.Rd
+++ b/man/GeneExpSE.Rd
@@ -30,6 +30,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpDESeq2}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/consensusClusters.Rd b/man/consensusClusters.Rd
index 0e920be..1cb0bc6 100644
--- a/man/consensusClusters.Rd
+++ b/man/consensusClusters.Rd
@@ -60,6 +60,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpDESeq2}()},
 \code{\link{GeneExpSE}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/expressionClasses.Rd b/man/expressionClasses.Rd
index ef0aaf4..4f3774d 100644
--- a/man/expressionClasses.Rd
+++ b/man/expressionClasses.Rd
@@ -42,6 +42,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpDESeq2}()},
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/filteredCTSSidx.Rd b/man/filteredCTSSidx.Rd
new file mode 100644
index 0000000..e9ac091
--- /dev/null
+++ b/man/filteredCTSSidx.Rd
@@ -0,0 +1,53 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/GetMethods.R
+\name{filteredCTSSidx}
+\alias{filteredCTSSidx}
+\alias{filteredCTSSidx,CAGEexp-method}
+\title{The \code{filteredCTSSidx()} function is in \emph{CAGEr} functions to retrieve the
+result of the \code{flagLowExpCTSS()} function in a safe way.}
+\usage{
+filteredCTSSidx(object)
+
+\S4method{filteredCTSSidx}{CAGEexp}(object)
+}
+\arguments{
+\item{object}{A \code{\link{CAGEexp}} object}
+}
+\value{
+Returns the value of \code{filteredCTSSidx} in the row ranges of the
+tag count matrix experiment of the \code{CAGEexp} object, or \code{Rle(TRUE)} if it
+was \code{NULL}
+}
+\description{
+The \code{filteredCTSSidx()} function is in \emph{CAGEr} functions to retrieve the
+result of the \code{flagLowExpCTSS()} function in a safe way.
+}
+\examples{
+
+filteredCTSSidx(exampleCAGEexp)
+
+}
+\seealso{
+Other CAGEr filter functions: 
+\code{\link{flagByUpstreamSequences}()},
+\code{\link{flagLowExpCTSS}()}
+
+Other CAGEr accessor methods: 
+\code{\link{CTSScoordinatesGR}()},
+\code{\link{CTSScumulativesTagClusters}()},
+\code{\link{CTSSnormalizedTpmDF}()},
+\code{\link{CTSStagCountDF}()},
+\code{\link{GeneExpDESeq2}()},
+\code{\link{GeneExpSE}()},
+\code{\link{consensusClustersGR}()},
+\code{\link{expressionClasses}()},
+\code{\link{genomeName}()},
+\code{\link{inputFiles}()},
+\code{\link{inputFilesType}()},
+\code{\link{librarySizes}()},
+\code{\link{sampleLabels}()},
+\code{\link{seqNameTotalsSE}()},
+\code{\link{tagClustersGR}()}
+}
+\concept{CAGEr accessor methods}
+\concept{CAGEr filter functions}
diff --git a/man/flagByUpstreamSequences.Rd b/man/flagByUpstreamSequences.Rd
index f7d7f20..b5d6ac3 100644
--- a/man/flagByUpstreamSequences.Rd
+++ b/man/flagByUpstreamSequences.Rd
@@ -40,6 +40,11 @@ If the provided \code{object} represents \emph{tag clusters} or \emph{consensus
 the search will be done upstream its \emph{dominant peak}.  Convert the object
 to the \code{GRanges} class if this is not the behaviour you want.
 }
+\seealso{
+Other CAGEr filter functions: 
+\code{\link{filteredCTSSidx}()},
+\code{\link{flagLowExpCTSS}()}
+}
 \author{
 Charles Plessy
 }
diff --git a/man/flagLowExpCTSS.Rd b/man/flagLowExpCTSS.Rd
index 701a31e..797d69c 100644
--- a/man/flagLowExpCTSS.Rd
+++ b/man/flagLowExpCTSS.Rd
@@ -87,3 +87,9 @@ reproduced.
 \examples{
 flagLowExpCTSS(exampleCAGEexp, threshold = 100, nrPassThreshold = 2)
 }
+\seealso{
+Other CAGEr filter functions: 
+\code{\link{filteredCTSSidx}()},
+\code{\link{flagByUpstreamSequences}()}
+}
+\concept{CAGEr filter functions}
diff --git a/man/genomeName.Rd b/man/genomeName.Rd
index cbce7fd..61dc26c 100644
--- a/man/genomeName.Rd
+++ b/man/genomeName.Rd
@@ -52,6 +52,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
 \code{\link{librarySizes}()},
diff --git a/man/inputFiles.Rd b/man/inputFiles.Rd
index 1d3bb88..4f52f6d 100644
--- a/man/inputFiles.Rd
+++ b/man/inputFiles.Rd
@@ -41,6 +41,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFilesType}()},
 \code{\link{librarySizes}()},
diff --git a/man/inputFilesType.Rd b/man/inputFilesType.Rd
index acc4494..6cf8b35 100644
--- a/man/inputFilesType.Rd
+++ b/man/inputFilesType.Rd
@@ -75,6 +75,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{librarySizes}()},
diff --git a/man/librarySizes.Rd b/man/librarySizes.Rd
index 6a7711a..7689aa6 100644
--- a/man/librarySizes.Rd
+++ b/man/librarySizes.Rd
@@ -41,6 +41,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/sampleLabels.Rd b/man/sampleLabels.Rd
index 5b35997..ba59b5f 100644
--- a/man/sampleLabels.Rd
+++ b/man/sampleLabels.Rd
@@ -78,6 +78,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/seqNameTotalsSE.Rd b/man/seqNameTotalsSE.Rd
index b0eb9de..84c3207 100644
--- a/man/seqNameTotalsSE.Rd
+++ b/man/seqNameTotalsSE.Rd
@@ -39,6 +39,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},
diff --git a/man/tagClusters.Rd b/man/tagClusters.Rd
index 3046e32..93f7612 100644
--- a/man/tagClusters.Rd
+++ b/man/tagClusters.Rd
@@ -60,6 +60,7 @@ Other CAGEr accessor methods:
 \code{\link{GeneExpSE}()},
 \code{\link{consensusClustersGR}()},
 \code{\link{expressionClasses}()},
+\code{\link{filteredCTSSidx}()},
 \code{\link{genomeName}()},
 \code{\link{inputFiles}()},
 \code{\link{inputFilesType}()},