# HG changeset patch
# User proteomisc
# Date 1702742191 0
# Node ID 10e058addc0c27a8f9c753b9500e87d7139d0cd0
# Parent  dc0904796d06fa651a271a36c90fa77be6cc5372
Uploaded

diff -r dc0904796d06 -r 10e058addc0c preprocess_datasets/GenePix_Two_Colors_Preprocessing_Functions.R
--- a/preprocess_datasets/GenePix_Two_Colors_Preprocessing_Functions.R	Sat Dec 16 13:29:28 2023 +0000
+++ b/preprocess_datasets/GenePix_Two_Colors_Preprocessing_Functions.R	Sat Dec 16 15:56:31 2023 +0000
@@ -10,12 +10,11 @@
  MAb$M=(data_mt)
  MAb$A=NaRV.omit(as.data.frame(MAb$A))
  MAb$genes=(MAb$genes[(MAb$genes$ID %in% c(rownames(MAb$A),rownames(MAb$M))),])
- MA.avg <-suppressWarnings(suppressMessages(avereps(MAb, ID=MAb$genes$ID)))
+ MA.avg <-suppressWarnings(suppressMessages(avereps(MAb)))
  data_matrix=NaRV.omit(MA.avg$M)
  colnames(data_matrix)<-designo$sample
  write.table(format(data_matrix, justify="right"),sep="\t", quote=FALSE,
             row.names=T, col.names=T,file="Matrix.Data.tsv")    
 
 return(make_design(MA_matrix=list(dataBG=RG,dataNWA=RG.pq,dataNBA=MA.avg,matrix_data=as.matrix(data_matrix),symbol=MA.avg$genes$Name)))
-}
-
+}
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