search

ahmohamed / lipidr

Data Mining and Analysis of Lipidomics datasets in R
https://www.lipidr.org/
Other
27 stars 13 forks source link

Volcano plot eBayes f or t statistic #36

Closed annikaghub closed 2 years ago

annikaghub commented 2 years ago

Hi Ahmed,

when creating a volcano plot (plot_results_volcano), lipidr calls the eBayes function. I don't understand whether a moderated f or t statistic is computed/used. Can you tell me which one it is? Thank you for your time! Best,

Annika

ahmohamed commented 2 years ago

plot_results_volcano simply plot the results from limma::topTable (adj.P.Val and logFC). While I'm not sure exactly of the details, as per limma docs (https://rdrr.io/bioc/limma/man/toptable.html) below:

If coef has a single value, then the moderated t-statistics and p-values for that coefficient or contrast are used. If coef takes two or more values, the moderated F-statistics for that set of coefficients or contrasts are used.

P-values should be calculated based on moderated t statistics if you use contrasts (de_analysis), or when you specify a single coef in de_design (examples here and here). Alternatively, if you perform multigroup comparison (ANOVA-like), moderated F statistics will be used to calculate P-values (here).

You can view the topTable output from de_design and de_analysis, and examine whether a t or F statistic column is included, to be sure what was used for p-values calculations. You can also try LipidSuite Univariate analysis tab, which displays both the volcano plot along with the topTable interactively. There you'll see a t column when performing two-group comparison and F column when MultiGroup ANOVA is used.

Hope this answers your question. If not, feel free to reopen the issue. Cheers, Ahmed.

annikaghub commented 2 years ago

Perfect, thank you!