Question on the calculation of p values in volcano plots

ahmohamed / lipidr

Data Mining and Analysis of Lipidomics datasets in R

https://www.lipidr.org/

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Question on the calculation of p values in volcano plots #24

Closed vastevenson closed 2 years ago

vastevenson commented 2 years ago

Hi,

I am looking on lipidr.org, however I am not able to find a page that describes how the p values for the volcano plots are being generated. Can you please clarify?

Thank you!

-Vincent

ahmohamed commented 2 years ago

Hi @vastevenson, methods are described in detail in the paper. Basically, we use limma package under the hood (which does a moderated t-test). The p values are adjusted for multiple hypothesis testing.

PS: Can you please close the issues if you think they're resolved. Thanks!