XCMS in R August 21, 2019, 10:51:48 PM 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 rawdatacdffiles <-list.files("~/LCMS/cdf/Dave", recursive=T, full=T)xrms<-readMSData(cdffiles, mode = "onDisk", centroid= TRUE)but I have got this errorNo MS 1 data present.Then when I tried this code to create xcmsSet object, I received a similar errorError 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 Quote Selected
Re: XCMS in R Reply #1 – August 22, 2019, 03:04:30 AM 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 Quote Selected