How to reach to .. with XCMSnExp data?

[linlennypinawa]

I used to load the data files to xcmsSet data container, and get to diffreport().
Could you tell me the workflow with XCMSnExp data to get the same report?

[jorainer]

the diffreport is not available for XCMSnExp objects. With the updated workflow it's now suggested to call quantify on the results XCMSnExp which returns a SummarizedExperiment object (standard data container from Bioconductor) and then use any other tool or method to perform the statistical analysis. There are way better approaches available in R to do the statistical tests then diffreport did.

As alternative, there is still the possibility to convert the XCMSnExp to a xcmsSet object and then call the diffreport on that. To convert:

xset <- as(xdata, "xcmsSet")

where xdata would be your XCMSnExp object.

[linlennypinawa]

Thank you @jorainer. Would you please show me some resources of better approaches?

[jorainer]

One possibility would be Bioconductor's limma package - although it was developed originally for gene expression (microarray) data it works also good for metabolomics data. You can find the userguide here

[linlennypinawa]

One possibility would be Bioconductor's limma package - although it was developed originally for gene expression (microarray) data it works also good for metabolomics data. You can find the userguide here

Fantastic!