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Figure 1 | BMC Bioinformatics

Figure 1

From: Normalization and expression changes in predefined sets of proteins using 2D gel electrophoresis: A proteomic study of L-DOPA induced dyskinesia in an animal model of Parkinson's disease using DIGE

Figure 1

Boxplots of M or m values. Boxplots of the M or m-values for the 14 gels (A) before, and (B-E) after normalization using different methods. Gels are ordered (1–14) according to the experimental design in Table 1. For method A, B and E the M-values are calculated as log2Cy5/Cy3 and for method C and D the m-values are calculated as log2Cy5/Cy2 and log2Cy3/Cy2. For method C and D this results in two boxplots for each gel. After optimal normalization the M or m-values should average to zero and have approximately the same variance (equally high boxes) in all gels. The methods which are not illustrated in the figure show an impeccable pattern similar to that of (E).

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BMC Bioinformatics

ISSN: 1471-2105

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