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Topic: Hi, about: technical replicates average within xcmsSet created by xcms?  (Read 163 times) previous topic - next topic

  • gmhhope
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Hi, about: technical replicates average within xcmsSet created by xcms?
Hi,

I am currently working on a project to use X13CMS/geoRge to do stable isotope assisted un-targeted metabolomic analysis. Since the input require xcmsSet, I began with the running of xcms. But the problem came as followed:

We usually ran a sample 2/3 times in a machine to create technical replicates and then summarized by average/median. This is done usually by preprocessing after the creation of feature table after xcms/apLCMS. But for running X13CMS/geoRge, I need to use the original xcmsSet which I didn't figure out a way (or a xcms::function) to do the average of technical replicates within it.

I tried to modify the source code of X13CMS/geoRge to be able to adapt to my feature table which undergo the average of technical replicates. But this seems to be a very wasteful of my time.

Do you have any good suggestion about this? Or are you guys aware of any solution to it? Any suggestion will help! Great thanks!

Best regards,
Minghao Gong, PhD candidate
University of Florida
  • University of Florida