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 \
this is the command i write.
What is the problem in this script ?
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.
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.
That seems like a reasonably large sample size; I might consider filtering.
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
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.
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?
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.
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