diff --git a/R/SingleR.R b/R/SingleR.R
index 2d33145..a8bf931 100644
--- a/R/SingleR.R
+++ b/R/SingleR.R
@@ -114,7 +114,7 @@ SingleR <- function(
     for (rr in tmp.ref) {
         keep <- rownames(test) %in% rownames(rr)
         if (!all(keep)) {
-            test <- DelayedArray(test)[keep,,drop=FALSE]
+            test <- DelayedArray(test)[keep,,drop=FALSE] # only keeping the intersection, for safety's sake - see ?combineRecomputedResults.
         }
     }
     if (nrow(test) == 0) {
diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
index 4c0309d..264922e 100644
--- a/inst/NEWS.Rd
+++ b/inst/NEWS.Rd
@@ -8,6 +8,10 @@ This is also checked against \code{rownames(test)} in \code{classifySingleR()} t
 
 \item Restored the \code{BNPARAM=} argument in \code{trainSingleR()}, to enable more fine-grained specification of neighbor search algorithms.
 The \code{approximate=} argument is deprecated. 
+
+\item Soft-deprecated \code{check.missing=} in \code{classifySingleR()} and \code{combineRecomputedResults()}.
+This is because any filtering will cause a mismatch between the row names of \code{tests} and the \code{test.genes} in \code{trained}.
+Rather, filtering should be done prior to \code{trainSingleR()}, as is done in the main \code{SingleR()} function.
 }}
 
 \section{Version 2.0.0}{\itemize{