I just finished the "Introduction to DEP" tutorial which worked well for me. Now I am using the codes on my own data but because of my lack of replicates the following code from the tutorial gives an error when I use my own data:
datadiffmanual <- testdiff(dataimp, type = "manual", test = c("Ubi4vsCtrl", "Ubi6vsCtrl"))
Error in .ebayes(fit = fit, proportion = proportion, stdev.coef.lim = stdev.coef.lim, : No residual degrees of freedom in linear model fits
I am aware of why the error occurs(no replicates), my question is just how to change the code to treat 2 of my samples as replicates (different strains but uninduced, so they should be the same), so I can use this as a threshold for the statistics.
My experiment consists of two types of strains: WT and mutant. Each expressing either the protein of interest or a control-protein after induction. I have 3 timepoints in total: uninduced, induced-timepoint1, induced-timepoint2, so in total 12 samples. So the plan is to treat the 2 WT strains in the uninduced condition as replicates to get a dispersion(?) to use as the threshold for differentially "expressed" proteins.
I would be very thankful for any kind of help!