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.
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
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
