From 0fd3b4c8125102c3e4f090f1eac94b9705a5f8b3 Mon Sep 17 00:00:00 2001
From: Arsham Mikaeili Namini <92790984+Arshammik@users.noreply.github.com>
Date: Sun, 16 Nov 2025 04:18:14 -0500
Subject: [PATCH] Fix integer overflow in sigma2 initialization for large
 datasets
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Convert N and J to numeric before multiplication to prevent overflow
when N * J exceeds 2^31-1 (e.g., 4M cells × 20K genes = 80B).
---
 DESCRIPTION    | 4 ++--
 R/gedi_class.R | 3 ++-
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4ce9ea0..acfcff5 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: gedi
 Type: Package
 Title: Gene Expression Data Integration
-Version: 2.2.8
-Date: 2025-10-13
+Version: 2.2.9
+Date: 2025-11-16
 Authors@R: c(
     person("Arsham", "Mikaeili Namini", email = "arsham.mikaeilinamini@mail.mcgill.ca", role = c("aut", "cre")),
     person("Hamed", "S.Najafabadi", email = "hamed.najafabadi@mcgill.ca", role = c("aut"))
diff --git a/R/gedi_class.R b/R/gedi_class.R
index ec4a53f..27a568b 100644
--- a/R/gedi_class.R
+++ b/R/gedi_class.R
@@ -297,7 +297,8 @@ GEDI <- R6Class(
       # Initialize sigma2_0
       if (obs_type != "X") {
         Yp_full <- Y_log_dense - VecVecProduct(J_vec, s_0) - o_0
-        sigma2_0 <- sum(Yp_full^2) / (N * J + 1)
+        # Fix integer overflow: convert N and J to numeric before multiplication
+        sigma2_0 <- sum(Yp_full^2) / (as.numeric(N) * as.numeric(J) + 1)
       } else {
         sigma2_0 <- 1
       }