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sneumann
Topic: Looking for help: Dimensions of profile matrices do not match !
Hey ,
I met some problem in using XC MS, I can not fix by myself now. I am looking for help in here.
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 in advance!
Hi, I think something went wrong here, can you close
and open as issue rather than pull request ?
Also, please include the output of sessionInfo()
Yours, Steffen
Codecov Report
Merging #400 into XChromatograms will not change coverage. The diff coverage is
n/a.
@@ Coverage Diff @@
## XChromatograms #400 +/- ##
===============================================
Coverage 49.17% 49.17%
===============================================
Files 79 79
Lines 19731 19731
===============================================
Hits 9702 9702
Misses 10029 10029
Continue to review full report at Codecov.
Legend - Click here to learn more
Δ = absolute <relative> (impact),ø = not affected,? = missing dataPowered by Codecov. Last update 5cd366a...5cd366a. Read the comment docs.
Codecov Report
:exclamation: No coverage uploaded for pull request base (
XChromatograms@d8c564c). Click here to learn what that means. The diff coverage isn/a.
@@ Coverage Diff @@
## XChromatograms #400 +/- ##
=================================================
Coverage ? 49.87%
=================================================
Files ? 78
Lines ? 20062
Branches ? 0
=================================================
Hits ? 10005
Misses ? 10057
Partials ? 0
Continue to review full report at Codecov.
Legend - Click here to learn more
Δ = absolute <relative> (impact),ø = not affected,? = missing dataPowered by Codecov. Last update d8c564c...c2f81df. Read the comment docs.
Codecov Report
:exclamation: No coverage uploaded for pull request base (
XChromatograms@d8c564c). Click here to learn what that means. The diff coverage isn/a.
@@ Coverage Diff @@
## XChromatograms #400 +/- ##
=================================================
Coverage ? 50.29%
=================================================
Files ? 77
Lines ? 20103
Branches ? 0
=================================================
Hits ? 10111
Misses ? 9992
Partials ? 0
Continue to review full report at Codecov.
Legend - Click here to learn more
Δ = absolute <relative> (impact),ø = not affected,? = missing dataPowered by Codecov. Last update d8c564c...9b067b9. Read the comment docs.
Codecov Report
:exclamation: No coverage uploaded for pull request base (
XChromatograms@d8c564c). Click here to learn what that means. The diff coverage isn/a.
@@ Coverage Diff @@
## XChromatograms #400 +/- ##
=================================================
Coverage ? 46.40%
=================================================
Files ? 78
Lines ? 20543
Branches ? 0
=================================================
Hits ? 9533
Misses ? 11010
Partials ? 0
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