Hi folks, I know that to "run edgeR without replication" has been a popular question, but I'd like to specify the situation I'm in.
I'd like to compare DGE from pair tumor/normal samples collected from multiple patients. Uniquelly, I'm less interested to generalize a pattern for the patient population but to focus on each patient. The DGE from each patient is to validate the MSMS data obtained from the same tissues.
Therefore I don't have a typical replicates. However, I have data from multiple patients. I wonder if I can take full advantage of the sample size, to generate a universal tagwise dispersion that I could export and use for the comparison between individual samples, to hopefully generate a p value.
So my questions would be:
Is it statistically meaningful to do so？ If yes, should all normal samples be used for global tagwise dispersion be calculated or should I include the tumor samples?
Codewise, how am I suppose to export and inport dispersion database?
Thank you very much. Field