I'm currently using the package to understand differential gene expression between nodes and I am having trouble understanding the output. I'm interested in the RASC knot and which genes are causing the cells to differentiate into the ABI2 and distal_secretory clusters. I'm including the results from the earlyDEtest for knots 3 and 4 as an example. Shouldn't there be no difference between lineage 1 and 2 since they both go to the distal secretory cluster? Shouldn't I see the same/similar results when comparing lineage 1 vs. 3 and 2 vs. 3? Any guidance/ advice would be very much appreciated! Also, please let me know if I need to correct something in my workflow.
I'm also including the curves, which are slightly different from the lineages in terms of the location of the knots. Is this why I have different values between lineages 1 and 2 for knots 3 and 4?
Hey tradeSeq developers and users,
I'm currently using the package to understand differential gene expression between nodes and I am having trouble understanding the output. I'm interested in the RASC knot and which genes are causing the cells to differentiate into the ABI2 and distal_secretory clusters. I'm including the results from the earlyDEtest for knots 3 and 4 as an example. Shouldn't there be no difference between lineage 1 and 2 since they both go to the distal secretory cluster? Shouldn't I see the same/similar results when comparing lineage 1 vs. 3 and 2 vs. 3? Any guidance/ advice would be very much appreciated! Also, please let me know if I need to correct something in my workflow.
Thank you!!