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Topics - genefisher

1
R / Looking for help: Dimensions of profile matrices do not match !
Hey Everyone,

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.
2
R / Help on PCA: Error in colMeans(x, na.rm = TRUE) : 'x' must be numeric
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

Thanks in advance for all your help.
3
XCMS - FAQ / Error in do_adjustRtime_peakGroups(peaks = peakmat, peakIndex = object@groupidx,
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

Many thanks!

Yuechen