diff --git a/R/fit.R b/R/fit.R
index 7006a33..a17a415 100644
--- a/R/fit.R
+++ b/R/fit.R
@@ -113,12 +113,16 @@ compute_logratio <- function(object, aggregate = c("mean", "sum", "none")) {
 
     aggregate <- match.arg(aggregate)
 
-    if (aggregate %in% c("sum", "none")) {
+    if (aggregate=="sum")) {
         ## Do aggregation even with option "none" to ensure 
         ## matching ordering of eids in logr and log_dna
         dna <- getDNA(object, aggregate = TRUE)
         rna <- getRNA(object, aggregate = TRUE)
         logr <- log2(rna + 1) - log2(dna + 1)
+	} else if (aggregate=="none") {
+        dna <- getDNA(object, aggregate = FALSE)
+        rna <- getRNA(object, aggregate = FALSE)
+        logr <- log2(rna + 1) - log2(dna + 1)
     } else if (aggregate=="mean") {
         dna <- getDNA(object, aggregate = FALSE)
         rna <- getRNA(object, aggregate = FALSE)
diff --git a/R/mpra_set.R b/R/mpra_set.R
index 6d68e9c..3325038 100644
--- a/R/mpra_set.R
+++ b/R/mpra_set.R
@@ -21,6 +21,8 @@ setValidity("MPRASet", function(object) {
 MPRASet <- function(DNA = new("matrix"), RNA = new("matrix"),
                     barcode = new("character"), eid = new("character"),
                     eseq = new("character"), ...) {
+	DNA <- DNA[eid,]
+	RNA <- RNA[eid,]
     assays <- SimpleList(DNA = DNA, RNA = RNA)
     if (length(barcode)==0 & length(eseq)==0) {
         rowData <- DataFrame(eid = eid)