My data is univariate like the following. I want to find out taxa associated with control and disease groups:
I have run MetaPhlAn output with both Lefse (from galaxy) and Maaslin. I have used the command:
$ Maaslin2.R --transform=NONE --fixed_effects="type,subject" --normalization=NONE --standardize=FALSE cleaned_file_trans.tsv metadata.tsv /media/deep/New\ Volume/obesity/done/prjeb_7854_wgs_analysed/maaslin2/
Is my command correct?
I have got total 35 significant results (P<0.05) (6 disease enriched, 29 control enriched) when used LefSe. But, no significant result with MaasLin2 with the above command. When I used
--transform=LOG, I got only 5 significant results. They are common with the LefSe output and all from control enriched group. Why such discrepancy I am seeing in the result? Should I stop using Maaslin and only go with LefSe or am I doing some mistake with my commands?