The case for well-conducted experiments to validate statistical protocols for 2D gels: different pre-processing = different lists of significant proteins

Table 11 Comparing averaging across replicates versus not.

Averaged across replicates (54% of identified spots picked up)	Log Normalized Log Transformed Missing replaced with – 17.28 (100% of identified spots picked up)
SSP 1134	SSP 1134
SSP 1509	SSP 1509
SSP 1733	SSP 1733
	SSP 2309
SSP 2864
SSP 3222
	SSP 3219
	SSP 3806
	SSP 4203
SSP 4225	SSP 4225
	SSP 4435
	SSP 4724
SSP 5413	SSP 5413
	SSP 6205
SSP 6236
	SSP 6304
SSP 6314	SSP 6314
SSP 6349
SSP 6452	SSP 6452
SSP 7144
	SSP 7223
SSP 7439
SSP 7750	SSP 7750

Column 1 has the results of two sample t-tests when the intensity values were averaged across replicates. Columns 2 represents results of two sample t-tests when replicates were treated as independent observations.

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