Hi everybody! I’m sorry if this sounds like a silly question but I’m currently trying to do differential expression analysis (using both MTX and MGX data) of a microbial community using MTXmodel v1.2.4. While I understand the output coefficients (‘coef’) in the significant_result.tsv file indicate the effect size, I would like to express the difference in the expression of the two populations in the form of Log2(Fold Change) so as to be able to interpret the results better. Is it possible to directly make the conversion? I have attached the code I used for DE analysis below:
library(MTXmodel)
input_data ← ‘mtx_data_RELAB.tsv’
input_metadata <-‘metadata.tsv’
input_dnadata ← ‘mgx_data_RELAB.tsv’
fit_data ← MTXmodel(
input_data, input_metadata, ‘RESULTS’, transform = “LOG”,
fixed_effects = c(‘state’),
reference = “state,null”,
normalization = ‘NONE’,
standardize = FALSE,
input_dnadata = input_dnadata
)