I just downloaded XCMS from bioconductor and ran it according to the 'LC/MS Preprocessing and Analysis with xcms'. I had previously run the files I used for my test set in XCMSonline and I get very different outputs from the two methods. Specifically XCMSonline gives about 18,000 peaks where as the downloaded version gives 3,000. I ran both with their default parameters except I changed both 'full width at half maximum' parameters to match my chromatography. I was wondering if someone might be able to suggest a reason for this significant disparity.
Thanks for the help.
I might be able to help. I've experienced something similar and found that there was filtering going on when I wasn't expecting it in the group() command. If you include your code as well as what parameter settings you used online, I might be able to help.
Here is the r code I use:
raw_data_path = 'data_path'
raw_data = list.files(raw_data_path, recursive = TRUE, full.names = TRUE)
xset <- xcmsSet(raw_data, fwhm = 2)
xset <- group(xset)
xset2 <- retcor(xset, family = "symmetric")
xset2 <- group(xset2, bw = 10)
xset3 <- fillPeaks(xset2)
mydata = groupval(xset3, value="into")
write.csv(mydata, file = 'file_name)
In online xcms I started from the HPLC / Waters TOF parameter set and changed the following parameters:
ppm = 10
min peak width = 6
max peak width = 20
Thanks for your help
Kbz6,
On XCMS Online you can see what parameters you have used by viewing the parameter set or after the job is completed looking at the log file. The parameters below do not match the default XCMS Online Waters TOF parameter set. However, you may have changed these parameters. I would need the parameter id to know more specifically.
Cheers,
Paul
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