Figure 2
From: Significance analysis of microarray for relative quantitation of LC/MS data in proteomics
Random fluctuation. The number of quantified PCS's of a protein is plotted against the log ratio of the average relative abundance of its biological triplicates (Aav, representing either ApH5av or ApH7av) over the relative abundance of its in silico pooled replicate (Ap, representing either ApH5p or ApH7p) for the pH5 and pH7 samples respectively. The red diamonds and the small red dots represent the pH5 sample. The blue diamonds and the small blue dots represent the pH7 sample. The diamond symbols represent the average number of PCS's of a protein of the biological triplicates. The small dots represent the number of total PCS's of a protein in the in silico pooled replicates. The histograms based on the number of quantified proteins are also plotted, with the red trace representing the pH5 sample and the blue trace representing the pH7 sample.