I have two group to compare, I want to test if there is any significant difference. My specific question is should I search for the compound identification from data base, then compare or I can compare two data with the raw MS1 and MS2 mz values. The data was obtained from Synapt G2 in MSE mode. Please suggest some appropriate article or tutorial.
https://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html
And many more tutorials are available over the internet, check out in your search.
Volcano plot is generally obtained in univariate statistically analysis, while S-plot come from OPLS-da (a multivariate statistical analysis). Also, you can get S-plot only through the SIMCA software.
You can get a simil-Volcano plot in multivariate statistical tools creating a plot with the PLSda coefficients in the x-axis and the VIPs (variable importance in projection) in the y-axis.
But I think that first you should choose the type of statistical analysis you want perform...
regards
Why dont you use Markerlynx (part of Masslynx, Waters, USA). You can select your 2 data groups, perform PLSDA modelling and get the S-plot from there.
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