Entering edit mode
I am trying to conduct a differential expression (DE) analysis to identify enriched peptides in a phip-seq analysis using edgeR. However, as there are no replicates available, I am uncertain about how to determine the reliability of the BCV (square-root dispersion) utilized in the analysis. Since there is no established protocol for phip-seq analysis, I am unsure about the best approach for selecting this parameter. Is there a way to evaluate this factor?
Thank you so much in advance!
Not what you want to hear but the one truely reliable way is to do replicated experiments. For exploratory analysis you may simply choose the one suggested in the edgeR manual and see what the top hits are.
Thank you for your response. I completely agree with your point :). In the case of phip-seq, we cannot have a biological replicate, and unfortunately the technical replicate is not included in the experimental plan. I would like to know if the bcv value in edgeR manual (for RNA-seq analysis) can also be used for phip-seq?