From e0974cc898b35e89814e05258c573fd2a6f984af Mon Sep 17 00:00:00 2001
From: Tony Wu <wu.anthon@northeastern.edu>
Date: Fri, 13 Sep 2024 14:25:26 -0400
Subject: [PATCH] fix(dataProcessPlots): Remove duplicate log-transformation of
 intensity

---
 R/utils_dataProcessPlots.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/utils_dataProcessPlots.R b/R/utils_dataProcessPlots.R
index c74df44..05bd6cd 100644
--- a/R/utils_dataProcessPlots.R
+++ b/R/utils_dataProcessPlots.R
@@ -89,9 +89,6 @@
   ## Adjust colnames to avoid repeating code
   for (i in seq_along(data.list)) {
     colnames(data.list[[i]]) = toupper(colnames(data.list[[i]]))
-    if ('INTENSITY' %in% colnames(data.list[[i]])){
-      data.list[[i]]$ABUNDANCE = log2(data.list[[i]]$INTENSITY)
-    }
     setnames(data.list[[i]], c('LOGINTENSITIES', 'GROUP', 'PROTEIN', 
                                'Protein', 'LOG2INTENSITY'), 
              c('ABUNDANCE', 'CONDITION', 'PROTEINNAME', 'PROTEINNAME',
@@ -1755,4 +1752,4 @@
   if (address != FALSE) {
     dev.off()
   }
-}
\ No newline at end of file
+}