Print Page - Diffreport EIC's and scanrange

Title: Diffreport EIC's and scanrange
Post by: ozaslaver on February 25, 2013, 08:18:51 AM

Hello,

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

Title: Re: Diffreport EIC's and scanrange
Post by: sneumann on February 25, 2013, 01:20:57 PM

Hi,

1) which version of xcms is that ? 2) Can you reproduce the problem
with the faahKO data files ? Then we'll be able to see where the problem
comes from.

Yours,
Steffen

Metabolomics Society Forum

Software => R => XCMS => Topic started by: ozaslaver on February 25, 2013, 08:18:51 AM