I have a question that I can't seem to find an answer for this VIPER package. I was messing around with the regulon for the package, and at one point my regulon only contained one transcription factor (TF) with its target genes, the results I got back was kind of puzzling, where my TF activity score is all negative. My understanding for this VIPER package is that it infers the activity of the transcription factor with its target genes and normalize it in the end. So if I am only using only one TF, what does the negative activity score means and if normalization occurs, shouldn't the results be partially positive and partially negative?
I plotted out all the activity scores for that particular TF for each sample across time.
Also, eventually, I managed to include all my TFs into my regulon object, and ran VIPER with it. The activity score I got for that particular TF is still similar to when I first ran it.
