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Topic: XCMS in R (Read 73 times) previous topic - next topic

XCMS in R

Hello,

I'm new using LCMS to identify venom profiles. I'm trying to visualize and analyze data in R using XCMS. I have tried  with this code to read rawdata
cdffiles <-list.files("~/LCMS/cdf/Dave", recursive=T, full=T)
xrms<-readMSData(cdffiles, mode = "onDisk", centroid= TRUE)

but I have got this error
No MS 1 data present.

Then when I tried this code to create xcmsSet object, I received a similar error
Error in readRawData(fileName(object), includeMSn = includeMSn) :
  No MS1 data found in file C:/Users/jc554411/Documents/LCMS/cdf/Dave/A13.mzXML!

I export the data from the LCMS 2020 SHIDMAZU.

Can someone help me?

Thanks,

Linda  :)

 

Re: XCMS in R

Reply #1
Quadrupole instruments sometimes save data as chromatograms and not spectra.
You can try converting your original files with msconvert from Proteowizard and add: --simAsSpectra --srmAsSpectra
Blog: stanstrup.github.io