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Table 4 The effect of log transformation using non-normalized data.

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

No Log Transform Normalized, Missing replaced with zero (63% of identified spots picked up)

Log Transformed Normalized, Missing replaced with – 17.28 (100% of identified spots picked up)

 

SSP 1134

SSP 1509

SSP 1509

 

SSP 1733

SSP 2309

SSP 2309

 

SSP 3219

 

SSP 3806

 

SSP 4203

SSP 4225

SSP 4225

SSP 4435

SSP 4435

SSP 4519

 
 

SSP 4724

SSP 5309

 

SSP 5329

 

SSP 5413

SSP 5413

SSP 6205

SSP 6205

SSP 6228

 

SSP 6304

SSP 6304

SSP 6314

SSP 6314

SSP 6321

 

SSP 6349

 

SSP 6443

 

SSP 6452

SSP 6452

SSP 7223

SSP 7223

SSP 7334

 

SSP 7750

SSP 7750

SSP 8613

 
  1. Column 1 has spots that have significantly different intensities (p = 0.05) after normalizing and log transforming data. Column 2 has spots that are significantly different in intensity after normalizing data (using normalization 2), but after log transformation. The percentages in parenthesis in the header measure how many of the ten proteins known to be different were identified after log transformation and normalization.