1
R / Looking for help: Dimensions of profile matrices do not match !
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
Many thanks for you inadvance!
Have a nice weekend.