# HG changeset patch
# User proteomisc
# Date 1702733368 0
# Node ID dc0904796d06fa651a271a36c90fa77be6cc5372
# Parent  fadbdd8d76d5d7795e29ac4e037fba439b79452b
Uploaded

diff -r fadbdd8d76d5 -r dc0904796d06 preprocess_datasets/Agilent_Two_Colors_Preprocessing_Functions.R
--- a/preprocess_datasets/Agilent_Two_Colors_Preprocessing_Functions.R	Sat Dec 16 13:24:48 2023 +0000
+++ b/preprocess_datasets/Agilent_Two_Colors_Preprocessing_Functions.R	Sat Dec 16 13:29:28 2023 +0000
@@ -10,7 +10,8 @@
   MAb$A=NaRV.omit(as.data.frame(MAb$A))
   MAb$genes=(MAb$genes[(MAb$genes$ProbeName %in% c(rownames(MAb$A),rownames(MAb$M))),])
   RG.pq <<- RG.MA(MA)
-  MA.avg <- suppressWarnings(suppressMessages(avereps(MAb,ID=MAb$genes$ProbeName)))
+  MA.avg <- suppressWarnings(suppressMessages(avereps(MAb)))
+  #MA.avg <- suppressWarnings(suppressMessages(avereps(MAb,ID=MAb$genes$ProbeName)))
   data_matrix=NaRV.omit(MA.avg$M)
   colnames(data_matrix)<-designo$sample
   write.table(format(data_matrix, justify="right"),sep="\t", quote=FALSE,