How to obtain log2 intensity per sample in DEP?
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hele7 ▴ 20
@hele7-15035
Last seen 11 weeks ago
Estonia

Hi,

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?

Thanks ahead!

DEP • 94 views
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