W looks like =0

Hi,
I’m having problems with the interpretation of the volcano plot.
I think it's not this plot normal. All of them are the w=0.

qiime composition ancom \

--i-table comp_table.qza
--m-metadata-file metadata.txt
--m-metadata-column XXX
--o-visualization ANCOM_result/ancom_result_XXX.qzv

this is the command i write.


What is the problem in this script ?

Thanks!! Kei

Hi @fukui-ent-kei,

This typically happens when your sample size is small and/or you have a lot of features. (Although its more common when you have a small sample size.) What’s happening is that none of your p-values are small enough to overcome your FDR correction penalty.

One solution is to filter your data more judiciously, if you haven’t done so already. But, if your sample size is too small, it’s hard to correct that.

Best,
Justine

1 Like

Thanks, Justine!

I was very surprised that your precise reply was so fast.
In fact, I did ANCOM using table.qza and picrust_results made from 168 samples.

Is the number of samples small?
If not, filter more.

Thank you for your consideration.

kei

Hi @fukui-ent-kei,

That seems like a reasonably large sample size; I might consider filtering.

Best,
Justine

The sample size is large!
I thought it would be larger if it were an essay aimed at the environment.
I will work with confidence.

Thank you! kei

Hi @fukui-ent-kei,

One quick question: did you see a difference in any beta diversity metric you tested? Becuase if you didn’t see a difference in beta diversity, that might also be an issue.

Best,
Justine

Hi Justine,

There seems to be only one b-diversity after trying multiple items. Is there any difference in ANCOM because there is no difference in diversity?

thanks,
Kei

Hi @fukui-ent-kei,

Yes, if you dont have a difference in beta diversity, it’s unlikely you will see a difference in ANCOM; although it may depend on the metric you use.

Best,
Justine

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