Iterative Normalization Application Version 1.0

Requires Java 1.4.1.

This application reads in signal values from a datafile and normalizes based on the provided probeset list or all probes if no list is provided. It then finds probesets that do not change more than the threshold across chips [(max/min)<Threshold]. There are 2 output files for each iteration. One of the normalized values and one listing the unchanged genes. There is also a summary file.

This specific release of the program will overwrite output files {input filename}_ITER_{X} WITHOUT PROMPTING!

Datafile should be comma delimited with no quotes. For example:

Probe ID,Chip 1,Chip 2,Chip3,Chip4,Chip5,Chip6
204892_x_at,3665.099537,3397.39723,3466.237174,4053.097901,4596.780804,3919.030166
206559_x_at,4109.606975,3509.603291,3617.940649,3269.312599,4415.607552,4365.166931
207685_at,0.831448039,0.881079616,1.228548002,1.830890169,1.171694432,1.21085139
208645_s_at,2461.315938,2062.241219,2505.941888,3242.03703,2397.040135,2263.195658
208768_x_at,1649.921113,1798.7412,1948.55114,2229.132253,1756.739962,1772.838983
208825_x_at,4022.20647,3776.044056,3491.163377,4084.66902,3729.387749,3417.852102
208834_x_at,4113.326611,3829.538175,3496.654838,3975.578481,3593.617657,3530.432679
208856_x_at,2762.398589,2888.316293,2467.501657,1847.532491,2577.257531,2973.946355
208904_s_at,2323.065821,2161.8261,2218.565268,1853.647195,2543.75632,2340.575736


Unchanged Genelist file should be a text list with one probeset on each line. For Example:

200016_x_at
200017_at
200018_at
200025_s_at
200029_at
200031_s_at
200032_s_at
200034_s_at
200062_s_at

This application is released as-is. Technical bugs can be submitted to harbigjm@moffitt.usf.edu.
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