The bioBakery help forum

Question of normalization: LEfSe

Hi Galaxy team,

I am trying to upload and run LEfSe analysis at web page. And I found that the value after normalization to 1M is not equal to the relative abundance times 1M. Using the feature below as example:

asS’k__Bacteria.p__Firmicutes.c__Erysipelotrichi.o__Erysipelotrichales.f__Erysipelotrichaceae.g__Coprobacillus.s__’

The relative abundance value: aF0.000167604

If directly times 1M from relative abundance: 167.604

Normalized value from LEfSe: aF1933.3784461892012

From what I understand, the relative abundance per sample sums to 1, so if normalize per sample by 1M, I should be able to get the value after multiply by 1M. So I don’t get what happened in the middle. I format the data just like the example data set. It will be appreciated to get any replies.

Thanks!

Thanks for reaching out to the bioBakery Lab. Would it be possible for you to provide the input tables ? You would be able to attach the files here in the forum.

Regards,
Sagun