From 6c030679b73cbd46b2b496906ffe7b449c5776aa Mon Sep 17 00:00:00 2001
From: MA-Tianrui <tianruim@umich.edu>
Date: Tue, 19 May 2026 13:55:06 -0400
Subject: [PATCH] Add validation in dep() to catch error when every condition
 has only one replicate

---
 server.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/server.R b/server.R
index 785e04e..7266083 100644
--- a/server.R
+++ b/server.R
@@ -935,6 +935,14 @@ server <- function(input, output, session) {
          "QC plots (PCA, sample correlation, missing values, etc.) are still available."
        )
      ))
+     validate(need(
+       ncol(data) > length(conditions),
+       paste0(
+         "Differential expression analysis requires at least 2 replicates per condition. ",
+         "The current design has ", length(conditions), " condition(s) across ", ncol(data), " sample(s), ",
+         "leaving no residual degrees of freedom for variance estimation."
+       )
+     ))
      if (input$exp == "LFQ" & input$lfq_type == "Spectral Count") {
        assay(data) <- log2(assay(data))
      } else if (input$exp == "LFQ-peptide" & input$lfq_pept_type == "Spectral Count") {