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Table 5 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 (54% of identified spots picked up) No Log Transform – Normalization 1 Missing replaced with zero (54% of identified spots picked up) No Log Transform Normalization 2, Missing replaced with zero (54% of identified spots picked up) No Log Transform Normalized-PDQUEST (64% of identified spots picked up)
    SSP 03121
    SSP 11121
    SSP 1309
    SSP 13211
    SSP13311
SSP 1509 SSP 1509 SSP 1509  
SSP 1733 SSP 1733   
    SSP 2307
   SSP 2309 SSP 2309
    SSP 32341
    SSP 34371
    SSP 35231
SSP 4225 SSP 4225 SSP 4225 SSP 4225
SSP 4435 SSP 4435 SSP 4435  
SSP 4438 SSP 4438   SSP 44382
    SSP 45171
SSP 4519 SSP 4519 SSP 4519 SSP 45192
    SSP 4637 2
SSP 4724 SSP 4724   SSP 4724
    SSP 47351
    SSP 50111
   SSP 5309  
   SSP 5329  
SSP 5413 SSP 5413 SSP 5413 SSP 5413
   SSP 6205  
   SSP 6304  
SSP 6314   SSP 6314 SSP 6314
   SSP 6321  
   SSP 6349  
   SSP 6443  
SSP 6452 SSP 6452 SSP 6452 SSP 6452
   SSP 7027  
    SSP 7231
   SSP 7223  
   SSP 7334  
    SSP 74131
   SSP 7750  
   SSP 8613  
  1. 1 These are spots that were present in a very small number of gels, and therefore did not meet our criteria to be included.
  2. 2 These spots have highly skewed distributions or were very poor quality spots. Log transformation made out the distribution closer to normal and p-values were no longer significant.
  3. Column 1 has spots that have significantly different intensities (p = 0.05) normalizing and log transforming data. Column 2 has spots that are significantly different in intensity after using normalization 1, but before using a log transformation. Column 3 has spots that are significantly different in intensity after using normalization 2, but before using a log transformation. Column 4 has the results from the image analysis software PDQUEST, which has an option for normalizing but no log transformation. Columns 1 and 2 are subsets of the 201 spots in the final data set that met our criteria for inclusion. Column 3 is a subset of all possible spots 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. The percentages in parenthesis in the header measure how many of the ten proteins known to be different were identified after the different normalization techniques.