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

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

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
  1. 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.