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

Table 8 Test results of log transformed intensities pre-and post normalization – Imputation Method 2

Normalization 1 Minimum replaced by Random sample of minimum from all 30 gels Log transformed (36% of identified spots picked up)	Normalization 2 Minimum replaced by Random sample of minimum from all 30 gels Log transformed (91% of identified spots picked up)
	SSP 1134
SSP 1509	SSP 1509
	SSP 1733
	SSP 2309
SSP 3806	SSP 3806
	SSP 4203
	SSP 4225
SSP 4435	SSP 4435
SSP 4724	SSP 4724
	SSP 5413
	SSP 6205
	SSP 6228
	SSP 6304
SSP 6314	SSP 6314
SSP 6452	SSP 6452
	SSP 7223
	SSP 7334
	SSP 7750

The table shows the results of two sample t-tests on log-transformed intensities, pre and post normalization, when each missing intensities in GSE or control gel were replaced by randomly selecting one of the 30 lowest spot intensity values from the 30 gels in the experiment. Spots in bold were later identified by MALDI-TOF. These were all spots that were biologically relevant to the system being studied.

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