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Messages - pdas

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XCMS - FAQ / Re: Why can you not compare multiple cases to a single control in XCMS?
Hello,

I have a similar issue, I'm rather new to xcms (and metabolomics in general) and would appreciate some clarifications.

I also have more than 1 sample class beside control, to build on the previous posts let them be class A, B, C (control). I organized them in subdirectories to allow for the automated classification, and I am following the standard protocol:

xcmsSet -> retcor -> group -> fillPeaks -> diffreport

diffreport is supposed to support only two class arguments "class1" and "class2", return t-test for those two classes and, if more classes are present, also perform anova.

The xcmsSets obtained processing A+C, B+C, A+B+C will all differ due to the applied corrections (e.g. I found a feature M162T72 become M162T73), and I guess there is not a "correct" one, but if I want in general to be able to compare all my samples, I should go for a consistent set of features and use xsetABC.

My questions is: is it correct to just run diffreport(xsetABC, "C", "A") and diffreport(xsetABC, "C", "B") or is there something else?

In particular, may I ask you Craig what you mean by "process each case against the control separately, rather than if I process both cases together with the control at the same time"? Is the same as what I mean by saying that I obtain either xsetAC, xsetBC, xsetABC?

Finally, is metaXCMS the option to go? In the published protocol they write "Although XCMS and other metabolomic programs that have been developed are well suited for the analysis of large sample numbers, the programs are limited in that they only compare two different sample groups directly". It sounds kind of definite that there is no other way than pairwise comparison.

Thanks!