It is my understanding that when making comparisons both within and between groups with paired samples, but there are a differing number of samples for each condition, the model matrix must be adjusted as such: C: DESeq2 paired and multi factor comparison
I am confused as to what removing elements from the model matrix means. Does this mean that I am losing information from paired samples that don't have a counterpart in the other condition? Am I throwing away information?
I apologize if my question is phrased poorly--I'm pretty confused and would appreciate any clarification. Thank you!