I am discovering the MaAsLin2 package.
I am doing a comparison of the metagenome of healthy volunteers (named CT) versus patients (named AML) using R and the latest release version of Maaslin2 (updated this morning). I would like to have the plots with the CT placed in the first column and the AML placed in the second column.
I followed the instructions found here.
Setting reference levels
But despite having the factors set at the right level, the output is still not correct.
Here are my R lines
mapping_T0$Group_ordered = factor(mapping_T0$Group, levels=c(“CT”,“AML”))
fit_data = Maaslin2(input_data = data.filter2, input_metadata = mapping_T0, output = “Maaslin2_with_filters”, fixed_effects = c(“Group_ordered”))
Factor w/ 2 levels “CT”,“AML”: 2 2 2 2 2 2 2 2 2 2 …
I saw the reference option here GitHub - biobakery/Maaslin2: MaAsLin2: Microbiome Multivariate Association with Linear Models and here Reference values for a categorical fixed effect variable but it seems to work only with factors of more than 2 levels.
I looked at similar posts, and didn’t find a solution. I hope I didn’t miss it.
Thanks for your input !
Looking forward to learning more about the package