differential expressed proteins cutoff threshold

Question

[dew]

Dear all,

May I know the threshold you used to define the significant DEPs(differential expressed proteins)? I see some papers used p < 0.05 & abs(fold change) > 1.3.

Is there a universal set or it depends on how many DEPs you can find: if few, then make the threshold a little loose, if many can use more strict?

Thanks a lot!

[Papyrus]

The values depend on what you want out of the study: you use the significance threshold to control the expected proportion of false positives in your results (ideally taking into account multiple testing); you use the fold change to select the changes of a magnitude that you consider to be biologically relevant.

In reality: IMO these boundaries are totally arbitrary and within the limits of reason you can try different settings if they allow you to discover meaningful biological results, as long as you clearly state your methods.

[dew]

Thanks a lot!