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Table 3 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 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
  1. 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.