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Figure 2 | BMC Bioinformatics

Figure 2

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 2

MA plots for gel 4 and 12. MA plots for gel 4 and 12 (A) before, and (B-E) after normalization using different methods. The average log2 intensity, A, is calculated as (log2Cy5+log2Cy3)/2. For method A, B, E, F and G the M-values are calculated as log2Cy5/Cy3 and for method C and D the M-values are calculated as log2(Cy5/Cy2)/(Cy3/Cy2). The red line in each plot shows the Lowess smoothing of the entire data in the plot and should ideally be a straight line on zero. The method by Kreil et al [10] gives intensity dependant bias in the low range in gel 4 and when the M values are calculated via the pool channel (Cy2, method C and D) the data tend to be more variable.

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BMC Bioinformatics

ISSN: 1471-2105

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