Skip to main content ↑ ↓

Messages

This section allows you to view all Messages made by this member. Note that you can only see Messages made in areas you currently have access to.

Messages - kbz6

1
XCMS / Re: Comparing XCMS batch version to XCMSonline
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
2
XCMS / Comparing XCMS batch version to XCMSonline
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.