From 59e6ba83edd8ab9e1d91bb3f5ec8fd175857c9a3 Mon Sep 17 00:00:00 2001
From: tonywu1999 <wu.anthon@northeastern.edu>
Date: Thu, 4 Dec 2025 14:42:39 -0500
Subject: [PATCH] fix(diann): Convert zeros to NAs

---
 R/converters_DIANNtoMSstatsFormat.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R
index 56d1bf0d..22d6223a 100644
--- a/R/converters_DIANNtoMSstatsFormat.R
+++ b/R/converters_DIANNtoMSstatsFormat.R
@@ -133,6 +133,7 @@ DIANNtoMSstatsFormat = function(input, annotation = NULL,
             summarize_multiple_psms = max),
         columns_to_fill = list(Fraction = 1,
                                IsotopeLabelType = "Light"))
+    input[, Intensity := ifelse(Intensity == 0, NA, Intensity)]
     
     input = MSstatsConvert::MSstatsBalancedDesign(input, feature_columns, 
                                                   fill_incomplete = FALSE,