The part I could not understand in ANCOM

I was trying to find out the features differ in abundance across different groups with ANCOM following “Moving picture tutorial”.

ANCOM assumes that few (less than about 25%) of the features are changing between groups. If you expect that more features are changing between your groups, you should not use ANCOM as it will be more error-prone (an increase in both Type I and Type II errors is possible).

I would like to know the details of this one sentence because I couldn’t
understand what it meant.

If someone would be so kind , could you please explain it clearly ?

Thank you.

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As I understood, if in your dataset abundances of more than 25% of features are changing between tested groups, it will affect theory testing. In one case, the correct null theory (no differences) may be rejected for some features, in other - test may fail to detect existing significant differences in features abundances. Or, false discovery rate increases and statistical power decreases.
But I have some doubts as well about this part:

Are they mean presence/absence differences or differences in abundances of only presented in all groups features :thinking: .

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Sorry for the late reply and thank you for your kind reply.

As you said, there are some questions that remain unanswered, but somehow I understand the meaning.

I’d like to do some more research myself.

Thank you.

Hi @yoshikisuzu and @timanix,

The 25% change assumes only 25% of the taxa have a change in relative abundance.

My suggestion (for what it’s worth) is (1) filter your data and (2) set a W value apriori rather than relying on the fancy significance. I think last I read, the ANCOM authors were recommending significant in 70% of comparisons, I tend to be slightly more conservative at 80%.



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