A benchmarking paper (Geistlinger et.al 2020) recommended PADOG as one of the preferred tools for geneset analysis when you have an expression matrix. I am currently implementing this method on our dataset and have encountered a question about the output that I could not find an answer to in the paper, the vignette, or the GitHub issues.
The output contains the following:
meanAbsT0: the mean of absolute t-scores
padog0: the mean of weighted absolute t-scores
I noticed that some of these values are negative. Given that a t-score can be negative, its absolute value should be positive. If I understood the paper correctly, the weights should also be positive, I am wondering how it is possible to have negative values in the output.
I would greatly appreciate any clarification you could provide on this matter. Thank you in advance for your time and assistance.