Please refer to our post guideline for such question. Here are some general comments:
For t-tests, make sure the input is the identical. MetaboAnalyst contains multiple steps for data processing & normalization steps - you can see the R command history below. You can get source code underlying these R functions from our MetaboAnalystR.
1. mSet<-InitDataObjects("conc", "stat", FALSE, 150)
2. mSet<-Read.TextData(mSet, "Replacing_with_your_file_path", "rowu", "disc");
3. mSet<-SanityCheckData(mSet)
4. mSet<-PerformSanityClosure (mSet);
5. mSet<-CheckContainsBlank(mSet)
6. mSet<-PreparePrenormData(mSet)
7. mSet<-Normalization(mSet, "NULL", "LogNorm", "AutoNorm", ratio=FALSE, ratioNum=20)
8. mSet<-PlotNormSummary(mSet, "norm_0_", "png", 150, width=NA)
9. mSet<-PlotSampleNormSummary(mSet, "snorm_0_", "png", 150, width=NA)
10. mSet<-Ttests.Anal(mSet, F, 0.05, FALSE, TRUE, "fdr", FALSE)