I used the core microbiome within the microbiome analyst and do not get detection thresholds over 1%. But within the data there are multiple ASVs with relative abundances of 1% and more.
I would suspect that there is no calculation to % (0 to 100) but only relative abundance (0 to 1)?
For example, OTU00005 (bottom of ASV table) should have a prevalence of 1 at 0.01 relative abundance % but is only at around 0.5 according to the color code.
Hello, the relative abundance in the core microbiome analysis is used to set the threshold of the relative abundance of the feature in a sample. The prevalence calculate the percentage of the samples in which the relative abundance of the given feature is over the threshold. For instance, the prevalence 0.5 of OTU00005 means that the relative abundance of OTU00005 is more than 0.01 in ~50% samples.
thank you for pointing out how the prevalence is calculated, I was wondering about how that works.
But that still leaves the question why there is no OTU detected in the core microbiome if the relative abundance threshold is at 1% or above. Because OTU00005 clearly has relative abundances of 1% and above (reaching up to 12%).
With the settings:
Sample threshold 10%
Relative abundance threshold 1%
I should at least get OTU00005 in the plot but I only get this error message:
Error No core features were detected using the current prevalence and relative abundance thresholds.