# HG changeset patch
# User ynewton
# Date 1348700963 14400
# Node ID 710627b479629fcefb3842e600292ab8319e431d
# Parent  31cfcab40d8fe76387efcc74b90a360a7cf746dd
Uploaded

diff -r 31cfcab40d8f -r 710627b47962 normalize.r
--- a/normalize.r	Wed Sep 26 17:32:30 2012 -0400
+++ b/normalize.r	Wed Sep 26 19:09:23 2012 -0400
@@ -126,9 +126,7 @@
 		normalized_normals <- unlist(lapply(normal_values, function(x){return((x - normal_mean)/normal_sd);}))
 		
 		tumor_values <- data_row[tumors_list]
-		tumor_mean <- mean(tumor_values)
-		tumor_sd <- sd(tumor_values)
-		normalized_tumors <- unlist(lapply(tumor_values, function(x){return((x - tumor_mean)/tumor_sd);}))
+		normalized_tumors <- unlist(lapply(tumor_values, function(x){return((x - normal_mean)/normal_sd);}))
 		
 		return(append(normalized_normals, normalized_tumors))
 	}
@@ -147,7 +145,7 @@
 	else if(dist == 'NORMAL'){
 		ranked_data_matrix <- apply(data_matrix,2,rankNA)
 		#return(apply(ranked_data_matrix, c(1,2), function(x){return(qnorm(mean=mean(x), sd=sd(x)));}))
-		return(apply(ranked_data_matrix, c(1,2), qnorm, mean=0, sd=2))
+		return(apply(ranked_data_matrix, c(1,2), qnorm, mean=0, sd=1))
 	}
 	else if(dist == 'WEIBULL_0.5'){
 		ranked_data_matrix <- apply(data_matrix,2,rankNA)