Volcano data with corrected value

MetaboAnalyst
1

I made a volcano and used the option y-axis p-value threshold 0.05 RAW (instead of p 0.1 by default set there). In this case i believe that it was not corrected. If i want to use corrected value there instead, then should i use p-value 0.05 and check the FDR option instead of raw? Please confirm

2

It literally means the p-values are FDR adjusted p values instead of raw p values.

3

Thanks for your comment. i am confused because when i chose the option FDR 0.1 or FDR 0.05 instead, nothing comes significant while if i calculate the adjusted p value (FDR) in excel, it shows me proteins which are significant on the adjusted p -value level.

4

Adding on, or you meant that the Volcano i made using option y-axis p-value threshold 0.05 RAW, is already the one having adjusted p value, please advise

5

If you choose FDR p-value, the p values will be FDR-adjusted. There is no other interpretation

In general, you should NOT compare results from Excel with those obtained from MetaboAnalyst, which is a comprehensive platform with many steps involved before actually computing the statistics. You can see the R command history to see the data processing and normalization steps.

6

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