I used DeSeq2 for testing differential abundance between my two groups, And got following results. I am aware about the limitation of use of DeSEq2 for differential abundance testing and ANCOM-BC2 being the appropriate method. However I am curiousabout the interpretation of this plot.
How come this genus is up as well as down regulated in the same group.? Does it make sense. I have other plot where the organism is ploted on negative as well as positive scale
I am not able to help with the interpretation of this unless you could provide more context!
What did you command did you run?
What is the legend for this figure?
Hi, I made this graph using Deseq2 package in R-studio following this Tutorial.
I am not sure how otu1 has two values. The plot in the tutorials also has similar result.
Thank you for your time.
The 'plot in the tutorial' has Genus along the x-axis, so it makes sense to have duplicates as multiple OTUs / ASVs / features will have the same genus.
In your case, your data has two features both called
Perhaps a bug?
Thanks for the explanation, the multiple dots for genus make sense. Just to be sure my this plot where I have ploted species against fold change might be a bug or something?
Thank you once again.
That graph makes more sense to me, because it's common to have two ASVs with the same species-level classification, but it's not common to have
OTU1 happen twice.
Perhaps there's a bug in some relabeling code that duplicated OTU1 unexpectedly?