Having run ProteoViz now several times from app.R as well as from the individual S1-S7 scripts under R4.1.0 and R4.1.1, I noticed that at the Volcano plots are not updated according to the parameters provided (FC, p-value cutoff):
Initially the plot is shown with FC=0 and -log p = 1
All data points are shown in black --> shouldn´t be the ones above the p-value cutoff marked with red color (as also shown in the ProteoViz paper)? Also, the dotted p-value cutoff line is not properly located at -log p = 1 but rather at -log p = 1.3
If I then alter the parameters to e.g. FC=2 and -log p = 2.5, the Volcano plot then adopts this appearance:
None of the dotted lines marking the corresponding cutoffs has changed positions, and - as before - the data points that would result as significantly changed (FC=2 and -log p = 2.5) are not marked in red.
I guess this is not the expected way how ProteoViz should work?
Having run ProteoViz now several times from app.R as well as from the individual S1-S7 scripts under R4.1.0 and R4.1.1, I noticed that at the Volcano plots are not updated according to the parameters provided (FC, p-value cutoff): Initially the plot is shown with FC=0 and -log p = 1
All data points are shown in black --> shouldn´t be the ones above the p-value cutoff marked with red color (as also shown in the ProteoViz paper)? Also, the dotted p-value cutoff line is not properly located at -log p = 1 but rather at -log p = 1.3
If I then alter the parameters to e.g. FC=2 and -log p = 2.5, the Volcano plot then adopts this appearance:
None of the dotted lines marking the corresponding cutoffs has changed positions, and - as before - the data points that would result as significantly changed (FC=2 and -log p = 2.5) are not marked in red.
I guess this is not the expected way how ProteoViz should work?
Best,
Hannes