The package help mentioned that it doesn't use ordinary t-test. I checked the code of
de_analysis(), and it seems that it's passing data to lmFit(). The result of
de_analysis() includes P-value and adjust P-value. How are they calculated? And can I use this to check if the concentration of a lipid species is changed significantly between 2 groups of samples?
BTW, my input data is absolute lipid concentration (nmol/10million cells). Do I have to normalize the data using
normalize_pqn()? Could anyone tell me under what circumstances should normalization be used?
I have removed the "limma" tag. Although lipidr uses limma under the hood, I can't answer questions about lipidr or what it includes as output.
If you check the source code of
de-analysis.Rline 135, you see it used
topTable, so type
?topTableto learn about its parameters. Since
de-analysis.Rdoes not seem to give any other than the default parameters, adj.p should represent the default BH-corrected p-values. The lines before 135 tell you how the differential analysis was performed (standard limma workflow).