LEFse error use frequency data from Qiime2 pipeline.

Hello, my problem was posted at biostar but no one answer yet. I hope I can get some help here. This is my post at biostar. I tried to replace 0.0 with 0.0000000000000000001 but this error still happened. Thanks.

Hi @11118,
While I haven’t used the LEfSE tool personally (only seen its pretty results) I’m guessing your problem is coming from formatting issues and not with the too many zeros issue as you point out. Sparsity is the name of the game with this type of data so I’m guessing they would be well aware of that in their design. In the sample of your biom table you posted I don’t see any class, subclass, or sample id fields which I believe are needed. If help doesn’t arrive here, you may also be able to recruit help if you post directly on the LEfSE google group forum.
Good luck!

Thanks @Mehrbod_Estaki . I did add class, subclass row for my data but didn’t shown at my post(don’t want post too long). I use ANCOM now and I think ANCOM is good.