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XCMS / Diffreport EIC's and scanrange
I've been using the following approximate code in order to observe differences in metabolite accumulation between a mutant and a control sample:
Code: [Select]
Mutant<-list.files("files", recursive = TRUE, full.names = TRUE)
xset<-xcmsSet(Mutant, snthresh = 4)
xset2<-group(xset)
xset3<-fillPeaks(xset2)
report<-diffreport(xset3, "mutant", "control", "report", 1000, sortpval = TRUE, value = "into")However I wanted to limit my EICs to only those within a certain RT range. When I tried adding scanrange = c(196-2200) to the xcmsSet function my EICs come out looking funny: Having random lines zigzaging everywhere, and the areas adjacent to peaks are highlighted rather than the peaks themselves.
Can anyone please tell what I am doing wrong?
Thank you,
Olga