Table 5.
The effect of log transformation using non-normalized data.
| 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 46372 | |||
| 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 These are spots that were present in a very small number of gels, and therefore did not meet our criteria to be included.
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.
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.