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

Table 3 The effect of log transformation using non-normalized data.

No Log Transform No Normalization, Missing replaced with zero (55% of identified spots picked up)	Log Transformed No Normalization, Missing replaced with – 17.28 (55% of identified spots picked up)
SSP 1509	SSP 1509
SSP 1733
	SSP 2307
	SSP 3219
	SSP 3806
SSP 4225
SSP 4435	SSP 4435
SSP 4438
SSP 4519
SSP 4724
SSP 5413
SSP 6314	SSP 6314
SSP 6452	SSP 6452

Column 1 has spots that have significantly different intensities (p = 0.05) before normalizing and log transforming data. Column 2 has spots that are significantly different in intensity before normalizing data, but after using a log transformation. Spots in bold were later identified by MALDI-TOF. These were all spots that were biologically relevant to the system being studied. The percentages in parenthesis measure in the header indicate how many of the ten proteins known to be different were identified before log transformation.

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