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Table 6 T-Test results of log transformed intensities pre-and post normalization – Imputation Method 1

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

Normalization 1 Missing replaced by = -.17.28 Log transformed (36% of identified spots picked up)

Normalization 2 Missing replaced by = -17.28 Log transformed (100% of identified spots picked up)

 

SSP 1134

SSP 1509

SSP 1509

 

SSP 1733

 

SSP 2309

 

SSP 3219

SSP 3806

SSP 3806

 

SSP 4203

 

SSP 4225

SSP 4435

SSP 4435

SSP 4724

SSP 4724

 

SSP 5413

 

SSP 6205

 

SSP 6304

SSP 6314

SSP 6314

SSP 6452

SSP 6452

 

SSP 7223

 

SSP 7750

  1. The table shows the results of two sample t-tests on log-transformed intensities, pre and post normalization, when all missing intensities were replaced by the lowest intensity value in the experiment (-17.28). Spots in bold were later identified by MALDI-TOF. These were all spots that were biologically relevant to the system being studied.