Question regarding running XCMS and Camera in newest version of RStudio

March 29, 2024, 02:06:34 PM

Hello:

We used to run our analyses with the following script in RStudio.

“library(xcms)
xset<-xcmsSet(method="centWave", prefilter=c(0,0), ppm=15, peakwidth=c(5,20), snthr=2)
xset1<-retcor(xset, method="obiwarp", plottype=c("deviation"))
xset2<-group(xset1, bw=2, minfrac=0.5, mzwid=0.015)
xset3<-fillPeaks(xset2)
dr<-diffreport(xset3, filebase="file_name", eicmax=20)
library(CAMERA)
xset4<-xsAnnotate(xset3)
xset5<-groupFWHM(xset4, perfwhm=0.6)
xset6<-groupCorr(xset5)
xset7<-findIsotopes(xset6)
xset8<-findAdducts(xset7, polarity="negative")
write.csv(getPeaklist(xset8), file="file_name2.csv")”

This has stopped working when we installed the new version of RStudio.
I am not too familiar with coding and will appreciate some help here.

Thank you.