I use density method to analyze the data, It shows error:
> xset1 <- group(xset, method="density", minfrac=0.1, minsamp=1, bw=10, + mzwid=0.01, sleep=0.001) Processing 263643 mz slices ... OK > xset2 <- retcor(xset1, family= "s", plottype= "m", missing=1, extra=1, + span=1) Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx, : No peak groups found in the data for the provided settings > xset3 <- group(xset2, method="density", mzwid=0.01, sleep=0.001, + minfrac=0.1, minsamp=1, bw=5) Error in group(xset2, method = "density", mzwid = 0.01, sleep = 0.001, : object 'xset2' not found > xset4 <- fillPeaks(xset3) Error in fillPeaks(xset3) : object 'xset3' not found > an <- xsAnnotate(xset4) Error in xsAnnotate(xset4) : object 'xset4' not found > anF <- groupFWHM(an, perfwhm = 0.6) Error in groupFWHM(an, perfwhm = 0.6) : object 'an' not found > anI <- findIsotopes(anF, mzabs=0.01) Error in findIsotopes(anF, mzabs = 0.01) : object 'anF' not found > anIC <- groupCorr(anI, cor_eic_th=0.75) Error in groupCorr(anI, cor_eic_th = 0.75) : object 'anI' not found > anFA <- findAdducts(anIC, polarity="positive") Error in findAdducts(anIC, polarity = "positive") : object 'anIC' not found > write.csv(getPeaklist(anFA), file="data.csv") Error in getPeaklist(anFA) : object 'anFA' not found
Yes, I have try both: xset2 <- retcor(xset1, family= "s", plottype= "m", missing=1, extra=1, span=1) xset2<-retcor(xset1,method="obiwarp",profStep=0.1,plottype="deviation")
The XC MS shows the same error. Error in .local(object, ...) : Dimensions of profile matrices do not match ! Do I need to change some parameters to try it?
Many thanks for your reply, Jan. Yes, I use orbiwarp, I use both of rector and orbiwarp to try it, but it does`s works. Here is my R script, could you please help me to check what is the probelm? library (xcms) library (CAMERA) xset <- xcmsSet(method="centWave", ppm=20, snthresh=10, peakwidth=c(5,18)) xset1 <- group(xset, method="density", minfrac=0.1, minsamp=1, bw=10, mzwid=0.01, sleep=0.001) #xset2 <- retcor(xset1, family= "s", plottype= "m", missing=1, extra=1, span=1) xset2<-retcor(xset1,method="obiwarp",profStep=0.1,plottype="deviation") xset3 <- group(xset2, method="density", mzwid=0.01, sleep=0.001, minfrac=0.1, minsamp=1, bw=5) xset4 <- fillPeaks(xset3) an <- xsAnnotate(xset4) anF <- groupFWHM(an, perfwhm = 0.6) anI <- findIsotopes(anF, mzabs=0.01) anIC <- groupCorr(anI, cor_eic_th=0.75) anFA <- findAdducts(anIC, polarity="positive") write.csv(getPeaklist(anFA), file="data.csv")
I met very strange problem, I can not fix by myself now. I am urgently looking for help.
I divided my samples(650 samples) into two sub groups named mock and treatment and then put them into one folder to run XCMS.
When I run mock(325 samples) independently, the XC MS runs well and it works fine for me.
When I run treatment(325 samples) independently, the the XC MS also .runs well.
However, when I run mock and treatment samples(650 samples) together, the XC MS shows error as follows:
Control0h_L1-50_BD7_01_38715 Create profile matrix with method 'bin' and step 0.1 ... OK Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-51_BE7_01_38716 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-52_BF7_01_38717 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-53_BG7_01_38718 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-54_BH7_01_38719 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-55_BA8_01_38720 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-56_BB8_01_38721 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-57_BC8_01_38722 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-58_BD8_01_38723 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-59_BE8_01_38724 Create profile matrix with method 'bin' and step 0.1 ... OK Control0h_L1-6_BG1_01_38666 Create profile matrix with method 'bin' and step 0.1 ... OK Found gaps: cut scantime-vector at 1399.01 seconds Control0h_L1-60_BF8_01_38725 Create profile matrix with method 'bin' and step 0.1 ... OK Error in .local(object, ...) : Dimensions of profile matrices do not match ! > xset3 <- group(xset2, method="density", mzwid=0.01, sleep=0.001, + minfrac=0.1, minsamp=1, bw=5) Error in group(xset2, method = "density", mzwid = 0.01, sleep = 0.001, : object 'xset2' not found > xset4 <- fillPeaks(xset3) Error in fillPeaks(xset3) : object 'xset3' not found > an <- xsAnnotate(xset4) Error in xsAnnotate(xset4) : object 'xset4' not found > anF <- groupFWHM(an, perfwhm = 0.6) Error in groupFWHM(an, perfwhm = 0.6) : object 'an' not found > anI <- findIsotopes(anF, mzabs=0.01) Error in findIsotopes(anF, mzabs = 0.01) : object 'anF' not found > anIC <- groupCorr(anI, cor_eic_th=0.75) Error in groupCorr(anI, cor_eic_th = 0.75) : object 'anI' not found > anFA <- findAdducts(anIC, polarity="positive") Error in findAdducts(anIC, polarity = "positive") : object 'anIC' not found > write.csv(getPeaklist(anFA), file="data.csv") Error in getPeaklist(anFA) : object 'anFA' not found
Hi, Any body knows how to solve this R PCA problem? I`ve try many times, I still don`t know the reason. I hope somebody could help me When I type: > dtp<-prcomp(tdt,retx= TRUE,center= TRUE,scale= TRUE) Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric
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 method