Alpha Diversity measures are the same

(Ben) #1

Hello,

I have been running the qiime diversity alpha-rarefaction plugin to get metrics for chao1, goods_coverage, shannon, and observed_otus. For some of the projects that I have been running recently, some of the metrics have the same numbers. For one project, chao1 and goods_coverage had the same numbers and for another project chao1 and shannon had the same numbers. Is this a possible bug?

Thank you

(Matthew Ryan Dillon) #2

Hey there @bensarawichitr!

How about you provide us with some more context? Are you saying you saw the same values across different samples? Across different projects? Please take a few minutes to write something detailed up. Thanks! :t_rex:

(Ben) #3

Hello,

Here is an example of what I’m talking about:

image
image.png208×577 5.61 KB

The values are the same for each metric for the each sample. Having chao1 and observed_otus have the same value does not make any sense. In the other project the values of chao1 and shannon are the same for each sample.

(Matthew Ryan Dillon) #4

How are you generating the feature table used to compute these metrics? DADA2? Deblur? OTU Clustering?

(Matthew Ryan Dillon) #5

If you used DADA2 to produce your feature table, you should be aware that DADA2 does not produce singleton ASVs. Let’s take a look at the formula for chao1:

chao1=S_{obs}+\frac{F_1(F_1-1)}{2(F_2+1)}

where F1 and F2 are the count of singletons and doubletons, respectively.

This reduces to chao1=S_{obs} when F1 is zero, which is the case when using DADA2. I think that explains your results. TLDR, you probably shouldn’t compute chao1 on DADA2-produced ASV table. If you didn’t use DADA2, please let us know.