dear all!

I just started using the xcms package for metabolomics data analysis. I was however puzzled, or better said, did not understand the logic behind it. From intuition I was expecting the xcmsRaw class to represent the raw data and the xcmsSet the preprocessed data. While indeed that seems to be the case, there seems to be no way to get from a (list) of xcmsRaw classes to a xcmsSet object. I was expecting that a function like findPeaks would somehow return a xcmsSet but that was not the case. I actually would like (as I was used from microarray data and sequencing) to first look at the raw data, perform some quality controls and then process that raw data into the final data (which I thought might be the xcmsSet).

Is there a simple way to get from the raw data to the peak list data? I find it quite cumbersome to first load the raw data, do quality controls, and than basically re-load and process the raw data again (using the xcmsSet function) to generate the xcmsSet object.

thanks in advance for any help, suggestions etc

jo

Hi Johannes

What you're describing is the logic workflow, but not something that is readily possible in xcms. I guess one of the reasons is memory constrained - having all raw data read into memory at once is not really feasible in many scenarios.

A workaround is to use the write.mzdata to save you're changes to the raw data into new files, and then input these files into the xcmsSet function.

My main gripe with xcms is exactly the lack of direct link between raw and derived data, which is why I started working on MSsary. That project is unfortunately on hold at the moment but will be taken up as soon as possible.

I hope this helps you with your current work...