I'd need to obtain the log2 centered intensity values for specific proteins per each analyzed sample from DEP package (to generate plots outside of R).
According to the manual, this is how it should be done:
> plot_single(dep, proteins = "Saa4", type="centered", plot=FALSE) protein condition log2_intensity CI.L CI.R 1 Saa4 P4_i -1.04328583 -4.8053213 2.7187496 2 Saa4 P4_n 0.05337909 -0.9746904 1.0814486 3 Saa4 P5_i -0.92754466 -2.1226689 0.2675796 4 Saa4 P5_n -0.61831031 -2.4454895 1.2088689
Yet, the log2 intensities there are the MEAN values per each condition (P4_i, P4_n, P5_i, P5_n) whereas I'd need the log2 centered intensities per replicate/sample.
On the actual plot
plot_single(dep, proteins = "Saa4", type="centered", plot=TRUE) I can see the different replicates, but how can I retrieve the numeric data that is being plotted?