Ancom volcano plot

User Support
1

Dear users support,

I red the previous answers about the same problem with ancom probably due to a bug of qiime2 2018.06 as you wrote (the problem is that i can see both statistical results and percentile abundances but not volcano plot), so I installed Qiime2 core 2018.8 as you suggested to another user, but the problem persists although 2018.8. Could you help me please?

KInd regards,

Giuseppe Ancona

2

Thanks for reporting, @giuancona. Could you please share the visualizer that you generated? We will do some forensics on it to see what went wrong. Thanks!

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Screenshot%20(6)
Screenshot%20(6)1366Ă—768 213 KB

Thank you for the reply; here I attached the screenshot during Qiime2 2018.8; the same occured with Qiime2 2018.6.
I hope that you could help me,

Thank you very much

Giuseppe.

4

That visualization is clearly from 2018.6 or earlier — the multi-colored icon indicates that it was generated with bokeh, which we replaced with a different plotting tool in 2018.8. So it seems like either you are using 2018.6 or there is something wrong with your 2018.8 install. Could you please provide the output of the following command?

qiime info

Thanks!

5

Hi, thank you for reply.
You’re right because the file was generated with Qiime 2018.6, I haven’t tried again to generate another file with Qiime2 2018.8, but I only copied it from Qiime2 2018.6 to QIime2018.8 to try to open it with qiime tools view through Qiime2 2018.8 (because I though that it was possible after installation of qiime2 2018.8). So, if I understood well, I could generate it again (all pipeline: from demux to relative abundance analyses…) using only Qiime 2 2018.8 and after this, I could try again with ancom.

Thank you again,

Giuseppe

6

Incorrect. You do not need to run the whole pipeline again in 2018.8!

You do need to re-run ANCOM in 2018.8, however. The issue in 2018.6 was specifically with the plotting function used in that command, so the issue is isolated to that part of the command (the rest of the ANCOM results are valid). So just re-run in 2018.8 with your same data (processed in 2018.6) and it will work.

Good luck!

7

Hi,
you’re right because after the conversion from a comp-file to ancom-file with QIime2 2018.8, I could see everything. QIIME2 2018.8 works without problems!

Thank you very much for your help,

Kind regards,

Giuseppe.

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