Required programs:

Install python (version 2.1 or newer) www.python.org
Install Numeric Python numpy.sourceforge.net
Install R www-r-project.org

Program descriptions:

ai2gc: read a clontech Atlas ImageArray text report and output a 2
column genecluster format file.

gcs2r: read in several trials in genecluster format and output a csv
file for R

pairedtest: A shell script, chop the gcs2r csv file into individual
genes, then run a paired t test on each gene, printing the
significance test.

Sample session:

$ ai2gc trial1.txt > trial1.out
$ ai2gc trial2.txt > trial2.out
$ gcs2r trial1.out trial2.out > trials-1-2.out
$ pairedtest trials-1-2.out

GENE01 t = -0.8806, df = 1, p-value = 0.5404 
GENE02 t = 0.3225, df = 1, p-value = 0.8014 
GENE03 t = 0.8945, df = 1, p-value = 0.5354 
GENE04 t = 6.5598, df = 1, p-value = 0.0963 
GENE05 t = -0.9545, df = 1, p-value = 0.5148 
GENE06 t = -0.7546, df = 1, p-value = 0.5884 
GENE07 t = -0.1303, df = 1, p-value = 0.9175 
GENE08 t = 1.0167, df = 1, p-value = 0.4947 
GENE09 t = 0.0992, df = 1, p-value = 0.937 
GENE10 t = 1.1561, df = 1, p-value = 0.454