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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.