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Topic: Discrepancy between XCMS online and XCMS R-Package (Read 259 times) previous topic - next topic

  • Oihane AD
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Discrepancy between XCMS online and XCMS R-Package
Hi all,
I am doing a comparison between the XCMS online and XCMS R-Package (3.0.2) using exactly the same parameters. I have found that the results are not the same. What I have obtained is the following:  XCMS online reported 778 features in total while XCMS R-Package reported   572. If I removed features with RSD<20% (all the sample are QCs so I would expect all features to have low RSDs) then there are 417 and 374 features left for online and R-package respectively.

I also have done a Venn diagram to see the common features and the result is that 330 features (71.6%) are the same in both cases, 44 (9.5%) are unique for XCMS R-Package and 87 (18.9%) are unique for XCMS Online.

I feel such difference is interesting and a little bit strange.  Does anyone know what is behind this differences?

Thank you all,
Oihane

  • UniversIty

  • Jan Stanstrup
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  • Administrator
Re: Discrepancy between XCMS online and XCMS R-Package
Reply #1
Without knowing what version of XCMS is running on XCMS online it is probably impossible to guess.
If you can get that info and are sure all settings are 100% identical then maybe @johannes.rainer have some idea what change there could be.
  • University of Copenhagen, Denmark
Blog: stanstrup.github.io

  • Oihane AD
  • [*]
Re: Discrepancy between XCMS online and XCMS R-Package
Reply #2
The XCMS online results were obtained two days ago so I assume the version is the latest one. I could not find that info on the web site.
Thanks for your reply,
  • UniversIty