Version differences

Hi, LefSe version 1.0 and version 1.1.01 gives different result in command line (same parameters used).

Lefse analysis version 1.1.01 gives this result:
Number of significantly discriminative features: 117 ( 117 ) before internal wilcoxon
Number of discriminative features with abs LDA score > 2.0 : 66

Lefse analysis version 1 gives this result:
Number of significantly discriminative features: 26 ( 117 ) before internal wilcoxon
Number of discriminative features with abs LDA score > 2.0 : 26

I could not find the improvements applied on the new version, so I could not choose which version is better actually.

Can you comment on what is the differences in both versions of LEfSe?

Thanks in advance…

Hi @UGG ,
Thank you for reaching out to biobakery lab and apologies for getting back to you late.

Can you try using the latest version 1.1.2 of lefse please and let us know if you see any improvements? We do not support the older versions of lefse so we do recommend using the latest version 1.1.2.

Additionally, is it possible for you to point us at the LefSe version 1.0 and version 1.1.01 that you are using please (links)? I might have to reach out to the original authors of the tool to track down exact version differences on LDA scores.

Version 1.1.2

Regards,
Sagun

Hello,

I have installed LEfSe version 1.1.2 on our Linux server. To validate my installation, I tried to run the tutorial data (hmp_small_aerobiosis.txt) on Galaxy and on our Linux server using Galaxy’s default parameters. I found the results are different and I was not able to pinpoint the cause. I am attaching my results (LEfSe Results (Local Server vs Galaxy).xlsx) and I wonder if anyone can give me any suggestions on the cause?

I have considered that one possible cause is because of the software version differences, but I was not able to check the software versions on Galaxy, I believe only Galaxy administrators have the privilege to do that. I would be grateful if a bioBakery team member can provide me the software versions on Galaxy.

Version in Galaxy Version in Our Linux server
LEfSe ? 1.1.2
Python ? 3.9.6
rpy2 (python package) ? 3.4.5
R ? 4.1.1
survival (R package) ? 3.2.12
mvtnorm (R package) ? 1.1.2
modeltools (R package) ? 0.2.23
coin (R package) ? 1.4.1
MASS (R package) ? 7.3.54

Thanks & Regards,
Zita