Welch test

MetaboAnalyst
1

Hi all,

I am using MetaboAnalyst to make a volcano plot out of my lipidomics data. I calculated the Welch test in R (using rstatix library) and compared it to the one I got from Excel and from Python (output from stat library) and these all look the same.
When I calculate and plot it with MetaboAnalyst I get different p-values in Welch test, no clue why.
Does anyone have any idea?

Thanks

2

MetaboAnalyst is a comprehensive workflow, not just computing p value directly from the input. You can see how many steps were performed in the R command history before the volcano plot.