Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx, June 23, 2019, 10:39:03 AM Hey, Anybody knows how to solve this problem with XC-MS? It shows:> xset2 <- retcor(xset1, family= "s", plottype= "m", missing=1, extra=1,+ span=1)Performing retention time correction using 2 peak groups.Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx, : Not enough peak groups even for linear smoothing available!In addition: Warning message:In do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx, : Too few peak groups for 'loess', reverting to linear methodMany thanks!Yuechen
Re: Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx, Reply #1 – June 23, 2019, 01:06:26 PM Dear Yuechen,the *peak density* alignment method requires a certain number of features (AKA grouped peaks) across all samples to perform the alignment. Without knowing more about your data it is pretty hard to tell what the problem is. I'd suggest you redo the correspondence analysis (peak grouping) with less stringent settings and retry.Secondly: I would suggest that you switch over to the *new* user interface and functions (see https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html for details). There you will e.g. also have the possibility to do the alignment on a subset of samples (e.g. if you have QC samples) or to exclude blank samples from the alignment (these in fact could cause the problem described above).jo
Re: Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx, Reply #2 – June 24, 2019, 07:46:35 AM Dear Jo,Since it is my first time to use this forum, I was so excited when I notice your reply my message. Thank you so much for helping me solve the peoblem.I will try to do it with your suggestions.Many thanksYuechen 1 Likes
Re: Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx, Reply #3 – May 17, 2021, 02:43:07 AM Quote from: johannes.rainer on June 23, 2019, 01:06:26 PMDear Yuechen,the *peak density* alignment method requires a certain number of features (AKA grouped peaks) across all samples to perform the alignment. Without knowing more about your data it is pretty hard to tell what the problem is. I'd suggest you redo the correspondence analysis (peak grouping) with less stringent settings and retry.Secondly: I would suggest that you switch over to the *new* user interface and functions (see https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html for details). There you will e.g. also have the possibility to do the alignment on a subset of samples (e.g. if you have QC samples) or to exclude blank samples from the alignment (these in fact could cause the problem described above).joHi Johannes,I suffered the same problems in peak alignment that complained too few peak groups, it happened when my samples number more than 3000, but it worked fine for less than 3000 samples. there are two groups for all my data (pos and neg). I used internal standards to do normalization, and I do not have QC samples in my dataset. I need to process more than 5000 or even more samples in my study, now I am struggling with it, do you have any better solution for it? scripts I usedpdp <- PeakDensityParam(sampleGroups=xset_peaksIdentified@phenoData@data$sample_group, maxFeatures = 100, bw = 10, minFraction = 0.1, minSamples =1)xset_grouped_first <- groupChromPeaks(xset_peaksIdentified, param=pdp)# Runpgp <- PeakGroupsParam(smooth = "loess", span = 0.7, minFraction = 0.1, family = "gaussian", extraPeaks = 1)xset_aligned <- adjustRtime(xset_grouped_first, param=pgp)group again.......BestTingting