Microscopy spatial correction Files

############################## microscope smoothing script  #####################################
# This script takes an input table with the following format, usually copied from a spreadsheet.
# Please ensure that you have saved the input table using a text editor that uses standard line breaks
# Note that saving the file from excel often does not have standard line breaks. The file should be
# called "data.txt"
#
# plate ID <tab> row <tab> column <tab> ORF <tab> gene <tab> score <tab> score etc... as many scores as you like
# please include column headings in the first row, particularly if you have many scores.
# On the first line, the first column heading must be the word "Pad" (case not important), 
# otherwise the heading won't be recognised. Also on the first line should be headings for each of the scores
# that you are normalising. Here is an example input file, note the headings in the first row:
#
# Pad	Row		Column	ORF		Gene	Score 1		Score 2
# TR-7	A		1		YMR053C	STB2	4.536		0.345
#
#
# **** IN THIS VERSION OF THE SCRIPT ZERO VALUES ARE IGNORED AND ASSUMED TO BE BLANKS *****
# see line ~151 for this exclusion
#
# There can be any number of pads, and each pad can have any number of columns and up to 16 rows.
# Columns are numerical, where as rows are letters (A, B, C etc)
#
# The script adjusts the scores based upon column and row averages (median) relative to the median plate value
# The scores should be numerical not text, although the script makes some attempt to parse out text from the scores
# zero values should be ignored. The scores a finally all normalised relative to the median of all the data.
# 
#
# Written in 2013 by Peter Thorpe