If I set the LDA score below the default value of 2.0, is it still statistically reliable?

Yong_Dae · May 4, 2021, 6:33am

I understood about LEfSe analysis(KW, Wilcoxon), but still not sure that can I adjust the default score.

Our data shows very few different species in score>2.0 . (Independent variable is two, before and after.)
So I want to adjust the default score. There are no problem?

please help me.

mishort · May 14, 2021, 4:06pm

Hello,
It is fine to change the default value for the LDA score; it is a measure of effect size, not statistical significance. Any features plotted will be statistically different.
Best,
Meg

Topic		Replies	Views
Parameters in the lefse analysis LEfSe	1	1186	September 27, 2021
Can I reduces the default LefSe LDA score? At least how much LDA cut off should I consider to consider? LEfSe	0	625	January 8, 2021
LDA score cutoff changes slightly the LDA scores LEfSe	1	367	October 5, 2023
Issue while calculating LDA effect size LEfSe	1	687	June 10, 2021
Why the "class" and "LDA effect size" column for some taxa are empty while alpha value set to 1.0 for both tests? LEfSe	3	739	September 17, 2020

If I set the LDA score below the default value of 2.0, is it still statistically reliable?

Related Topics