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Fix integer overflow in sigma2 initialization for large datasets #21

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Merged
Arshammik merged 1 commit into from
Nov 17, 2025
Merged

Fix integer overflow in sigma2 initialization for large datasets #21

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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -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"))
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3 changes: 2 additions & 1 deletion R/gedi_class.R
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Expand Up @@ -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
}
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