Different Fold-change analysis results with the example data

[rocilia]

Thank you for developing this useful platform. I'm confused about the fold-change analysis using the example data "human_cachexia.csv", as it shows a totally different results with the tutoria.

Here is my code:
library(MetaboAnalystR)
mSet<-InitDataObjects("conc", "stat", FALSE)
mSet<-Read.TextData(mSet, "https://rest.xialab.ca/api/download/metaboanalyst/human_cachexia.csv", "rowu", "disc")
mSet<-SanityCheckData(mSet)
mSet<-FC.Anal(mSet, 2.0, 0, FALSE)
mSet<-PlotFC(mSet, "fc_0_", "png", 72, width=NA)
mSet$analSet$fc$fc.log
My results: (Only the first few metabolites are shown because the original result was too long)

mSet$analSet$fc$fc.log
1,6-Anhydro-beta-D-glucose 1-Methylnicotinamide 2-Aminobutyrate
-0.1954100 -0.3896700 0.1474700
2-Hydroxyisobutyrate 2-Oxoglutarate 3-Aminoisobutyrate
-0.1284500 0.5224200 -0.1579600
3-Hydroxybutyrate 3-Hydroxyisovalerate 3-Indoxylsulfate
0.4698100 0.5433300 -0.0894080
4-Hydroxyphenylacetate Acetate Acetone
-0.4816000 0.5679200 -1.0406000

The tutorial:

1,6-Anhydro-beta-D-glucose 1-Methylnicotinamide
0.888690 -0.052019
2-Aminobutyrate 2-Hydroxyisobutyrate
1.312700 0.633520
2-Oxoglutarate 3-Aminoisobutyrate
1.098400 1.329100
3-Hydroxybutyrate 3-Hydroxyisovalerate
1.563700 1.164900
3-Indoxylsulfate 4-Hydroxyphenylacetate
0.857170 0.263810

Thank you so much for your kind help!

[rocilia]

It shows the same result as the tutorial after column-wise normalization. However, as the tutorial recommends, FC is calculated as the ratio between two group means using the data before column-wise normalization was applied. So which method should I choose?