How does MetaboAnalyst calculate the fold change?

[DA17]

Hi,
Could you please explain me how MetaboAnalyst calculates the fold change between two groups of results?

On the “Fold Change Analysis” page of MetaboAnalyst, it is written that " FC calculation are using data before the column-wise normalization was applied (i.e. at the original scale)". → I assume we’re talking about the raw data.

It is also written that " For unpaired analysis, FCs are calculated as the ratios between two group means (M1/M2).". I tried to reproduce this calculation in Excel, by calculating for each metabolite separately the mean of group 1 and the mean of group 2, then dividing the results (M1/M2), but I could not recover the same results of FC as obtained previously in MetaboAnalyst.

I tried to upload again my data on MetaboAnalyst but without performing any normalization this time (choosing “none” everywhere during the normalization step). The Fold Change Analysis gave me the same results I obtained by myself in Excel. So it seems that MetaboAnalyst doesn’t use the raw data to calculate the means and the fold change.

So could you explain me the calculation steps please? Which data and which formula are used to perform the calculation?

Many thanks in advance for your help.

[jeff.xia]

MetaboAnalyst is a comprehensive web-based platform. Trying to reproduce it using Excel is in general not advised. It is unclear to me why people would like to do this. If you don’t trust the web interface, or would like to learn, the best alternative is using R. Every computing in MetaboAnalyst is done via R command and you can see the R command history (and MetaboAnalystR package) to find out exactly the formula

For fold change analysis, the page clearly states “using data before the column-wise normalization was applied”, which is not raw data. Specifically, “column-wise normalization” aims to adjust sample specific variations (volume differences, dilution factors, etc), which should be considered for fold change analysis

What happened after data upload and before column-wise normalization (see below)?