Data presented in tsv of diffreport September 27, 2012, 02:18:30 AM Hi,just a question about the peaks that will be presented in the tsv generated by the diffreport. I am comparing two groups (each having 3 samples). When I manually checked for the presence of a specific peak in one of the groups, I found it to be present in all samples of this group. Also the peak shape looked ok: peakwidth approximately 15 seconds and the retention time deviation between the samples was max 10 sec (determined at the apex of the peak). It's not a very abundant peak but clearly present (>10 scans, intensity > 1000 cpm). This is the script I used:xset<-xcmsSet(method="centWave", ppm=2.5, peakwidth=c(10,90), snthresh=25,mzdiff=0.01,prefilter=c(3,1000))xset<-group(xset, bw=10, mzwid=0.015,minfrac=0.5,minsamp=1)xset2<-retcor(xset,method="obiwarp",profStep=0.1)xset2<-group(xset2, bw=5, mzwid=0.015,minfrac=0.5,minsamp=1)xset3<-fillPeaks(xset2)Although the difference between the two groups was not statistically significant for this peak, I was expecting to find it at least back in the results.tsv file. Or am I wrong here?Koenp.s. I know that the peakwidth preferably should be something like c(15,90), but this also did not work out for this peak. Quote Selected
Re: Data presented in tsv of diffreport Reply #1 – October 08, 2012, 05:07:16 PM Yes, the diffreport contains all features, not just the dysregulated ones. Quote Selected
Topic: Data presented in tsv of diffreport