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XCMS Online / Re: Discrepancy between XCMS online and XCMS R-Package
Thanks for your reply,
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Messages - Oihane AD
Thanks for your reply,
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XCMS Online / Discrepancy between XCMS online and XCMS R-Package
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