--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/robustZScoreNormalization.pl	Wed Jun 01 03:59:51 2016 -0400
@@ -0,0 +1,76 @@
+###############################################################################
+# In summary this script calculates the robust z score for one or more plates
+# of data.
+#
+# Args:
+#   input.data.frame contains one or more columns of plate data. The first column 
+#   must contain the well annotation ie A01, A02 etc. Each subsequent column represents
+#   a plate of data where the column name is the plate name.
+#
+#   plate.conf.data.frame is a file of the following format:
+#	  well, type (syntax must be either "poscontr" or "negcontr" or "empty"), name (name of control)
+#
+# Returns:
+#    robust z score normalized values per plate.
+#
+# Author: kate gould
+###############################################################################
+
+use strict;
+use warnings;
+use IO::Handle;
+use File::Temp qw/ tempfile tempdir /;
+my $tdir = tempdir( CLEANUP => 0 );
+
+# check to make sure having correct input and output files
+my $usage = "usage: robustZScoreNormalization.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n";
+die $usage unless @ARGV == 3;
+
+#get the input arguments
+my $plateData = $ARGV[0];
+my $plateConfig =  $ARGV[1];
+my $zNorm =  $ARGV[2];
+
+#open the input files
+open (INPUT1, "<", $plateData) || die("Could not open file $plateData \n");
+open (INPUT2, "<", $plateConfig) || die("Could not open file $plateConfig \n");
+open (OUTPUT1, ">", $zNorm) || die("Could not open file $zNorm \n");
+
+#variable to store the name of the R script file
+my $r_script;
+
+# R script to implement the calcualtion of q-values based on multiple simultaneous tests p-values 	
+# construct an R script file and save it in a temp directory
+chdir $tdir;
+$r_script = "robustZScoreNormalization.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n"; 
+print Rcmd "
+	#options(show.error.messages = FALSE);
+	header <- read.table(\"$plateData\", head=F, sep=\"\\t\", comment=\"\", nrows=1);
+	input.data.frame <- read.table(\"$plateData\", head=F, sep=\"\\t\", skip=1);
+	plate.conf.data.frame <- read.table(\"$plateConfig\", head=T, sep=\"\\t\", comment=\"\");
+
+	# assumed second column is type ie negcontr or poscontr and third column is name of control
+	excluded.wells <- unique(plate.conf.data.frame[,1])
+	
+	robust.z.score.normalise <- function(x, y) return ((x-median(y))/mad(y))
+	robust.z.score.normalisation.data.frame <- data.frame(well=input.data.frame[,1], stringsAsFactors=FALSE)
+	
+	for (i in 2:length(colnames(input.data.frame))){
+		replicate.sample.values <- input.data.frame[((!(input.data.frame[,1] %in% excluded.wells))&(!(is.na(input.data.frame[,i])))),][,i]
+		robust.z.score.normalisation.data.frame <- cbind(robust.z.score.normalisation.data.frame, round(sapply(input.data.frame[,i], FUN=robust.z.score.normalise, replicate.sample.values), 2))
+	}
+	names(robust.z.score.normalisation.data.frame) <- names(input.data.frame)
+	write.table(header, file=\"$zNorm\", quote=F, sep=\"\\t\", row.names=F, col.names=F);
+	write.table(robust.z.score.normalisation.data.frame, file=\"$zNorm\", quote=F, sep=\"\\t\", row.names=F, col.names=F, append=T);
+	#eof\n";
+
+close Rcmd;	
+
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+
+#close the input and output files
+close(OUTPUT1);
+close(INPUT1);
+close(INPUT2);