I have a very simple question regarding some terminology.
When getting matrices from the xcmsSet object, I've read there are three options for [value] value = "into" value = "maxo" value = "index" ; which I think is also the default
I've read that "into" is for the integrated peak and "maxo" is for the maximum peak, however I am still confused with regards to what the "index" values mean? Any help would be greatly appreciated.
I have a question regarding XCMS and its treatment of multiple classes. For example, I have three groups of Data: control, 50ppm Ni treated samples, 150ppm Ni treated samples.
Is it possible to fit all of the three data in one xcms run in R, or should I only do them two at a time? I am planning to do PCA directly after the fillPeaks step.
Case (I): control, 50ppm and 150ppm -> xcms -> PCA
Case (II): control and 50ppm -> xcms 50ppm and 150ppm -> xcms control and 150ppm -> xcms then everything PCA
I was wondering if there is any way to perform OPLS (orthogonal partial least squares) in R? Or would anyone happen to know if there are any packages existing which can do OPLS on metabolomics data?
Good day everyone, I am new to the group and also new to metabolomics and xcms. I've tried out the guide in the "xcms cookbook" section regarding PCA & MDS. After getting the loadings plot with the text, which has the format x/y for each loading, where x and y is a real number (e.g. 313.3/1313), I was wondering how would you go about returning to the actual data to find the retention time for which this interesting feature elutes? If I am not mistaken, before PCA, the data was normalized, and after that the dimensions are reduced, if so how would you try to go back to the source of the interesting feature?
