LEfSe reporting a marker as significant when it isn't?

Downstream analysis and statistics LEfSe
1

Hi all,

I’ve been using the LEfSe tool to get some candidate enzymatic reactions that are different in my treatment groups. However, it looks like at least one of the hits (with a pretty hefty estimated effect size) isn’t actually significant at all (see EC_3_2_1_23) in the attached figure.

The raw values for this are the following (5 ABT_3wo followed by 3 UT ):
EC_3.2.1.23 23601.13 22159.68 24630.1 25438.25 24401.71 22057.87 22046.91 28232.54

Since the first filter is a rank-sum test for significance, I’m struggling to understand how it came up as a false positive.

Thanks so much for your help.

(upload://1ncQ2qzxXLfkaMtAXHTYlnJqf1P.png)

2

Hi there,

Just making sure that this doesn’t get completely buried. Any advice on the above would be extremely helpful, thanks so much.

3

Hi Kevin,

Apologies for my really late response. Can you re-load the png file. I can’t see it. Additionally, without seeing the raw data I am not sure how much help I can be. My guess would be is that the data is not reading-in correctly. Can you re-load the file and we can go forward from there?

Best,
Kelsey