Skip to main content
Topic: Discrepancy between XCMS online and XCMS R-Package (Read 661 times) previous topic - next topic

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


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.
Blog: stanstrup.github.io

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,

Re: Discrepancy between XCMS online and XCMS R-Package

Reply #3
Hi,

I have been trying to do a similar comparison recently with identical parameters using XCMS online (3.7.1 as displayed on their website) and the R package (version 3.4.2). I also get different results in terms of number of features. When I checked the log file created by XCMS online, I found the following header text:
------------------------------------------------------------------------
XCMSOnline  version  2.7.2
XCMS        version  1.47.3
CAMERA      version  1.34.0
------------------------------------------------------------------------

I am not sure why does XCMS online log file display old version numbers for XCMS online and XCMS. I have also reported this to the XCMS group via their contact form. 
Hope someone here can help me to make a fair comparison.

 

Re: Discrepancy between XCMS online and XCMS R-Package

Reply #4
AFAIK xcmsOnline uses an old version of xcms (that's what you see in the logs) - and most likely also an old version of R. The development of xcms and xcmsOnline somehow diverged at some point and all the new developments in xcms (aka xcms3) are not used/available in the online version.
 
Some discrepancies could eventually be explained by the changes in xcms that we did during the update and modernization (have also a look at the vignettes of xcms https://bioconductor.org/packages/release/bioc/html/xcms.html, specifically the New and modified functionality in xcms).

For a thourough comparison one would however have to start with an standalone R xcms version 1.47.3 and compare its results to those of xcmsOnline. Could be that xcmsOnline has some internal helper functions and modifications that are not available in the standalone R version of xcms ... but I am only guessing here.