Hello,
I recently start to use xcms for GC-MS data processing. When I used the example package "faahKO" with the instructed commen line everything worked. However when I try to use my own mzXML file, R studio gave me this error
> cdffiles
[1] ".//Control/BE-C1.mzXML" ".//Control/BE-C2.mzXML" ".//Control/BE-C3.mzXML"
[4] ".//Drought/BE-D1.mzXML" ".//Drought/BE-D2.mzXML" ".//Drought/BE-D3.mzXML"
> xset <- xcmsSet(cdffiles) # peak picking (step 2)
Error in xcmsSet(cdffiles) :
Chromatographic peak detection failed for all files! The first error was: Error in object@backend$getPeakList(x): [SpectrumList_mzXML::HandlerPeaks] Invalid pair order.
I am not sure what is happening. I load the xcms library already but this happened still. Another person using R 3.3.0 did not encounter this issue while other people use R 3.5.0 experienced the same thing. Is this version issue?
Here is the required output
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] xcms_3.2.0 MSnbase_2.6.1 ProtGenerics_1.12.0 mzR_2.14.0
[5] Rcpp_0.12.17 BiocParallel_1.14.1 Biobase_2.40.0 BiocGenerics_0.26.0
loaded via a namespace (and not attached):
[1] pillar_1.2.3 compiler_3.5.0 BiocInstaller_1.30.0 RColorBrewer_1.1-2
[5] plyr_1.8.4 iterators_1.0.9 tools_3.5.0 zlibbioc_1.26.0
[9] MALDIquant_1.17 digest_0.6.15 preprocessCore_1.42.0 tibble_1.4.2
[13] gtable_0.2.0 lattice_0.20-35 rlang_0.2.1 Matrix_1.2-14
[17] foreach_1.4.4 S4Vectors_0.18.3 IRanges_2.14.10 stats4_3.5.0
[21] multtest_2.36.0 grid_3.5.0 impute_1.54.0 survival_2.41-3
[25] XML_3.98-1.11 RANN_2.5.1 limma_3.36.2 ggplot2_2.2.1
[29] splines_3.5.0 scales_0.5.0 pcaMethods_1.72.0 codetools_0.2-15
[33] MASS_7.3-49 MassSpecWavelet_1.46.0 mzID_1.18.0 colorspace_1.3-2
[37] affy_1.58.0 lazyeval_0.2.1 munsell_0.5.0 doParallel_1.0.11
[41] vsn_3.48.1 affyio_1.50.0
From the error message I'd say there is a problem in reading your files. Some time ago we switched from mzML/mzXML data import using the Ramp backend to the proteowizard libraries (because they represent the standard implementation of the mzML format).
Could you please try the following:
And report the results?
Another suggestion: please use the newer xcms functions for data handling and analysis (instead of the xcmsSet function). Have a look at the xcms vignette for more information.
Hello,
Thanks for your help.
The error message showed up like this.
> library(mzR)
> fh <- openMSfile(".//Control/BE-C1.mzXML", backend = "pwiz")
Error in openMSfile(".//Control/BE-C1.mzXML", backend = "pwiz") :
File .//Control/BE-C1.mzXML not found.
> setwd("C:/Users/yuchiu/Google Drive/WVU/2018 Summer/PLSC593A Introduction to Metabolomics/test/test")
> fh <- openMSfile(".//Control/BE-C1.mzXML", backend = "pwiz")
> hdr <- mzR::header(fh)
> nrow(hdr)
[1] 5835
> spctr <- mzR::peaks(fh)
Error in object@backend$getPeakList(x) :
[SpectrumList_mzXML::HandlerPeaks] Invalid pair order.
I also see this warning message when I try to load library xcms
mzR has been built against a different Rcpp version (0.12.16)
than is installed on your system (0.12.17). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc support forum at
https://support.bioconductor.org/. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
1st, please re-install mzR using
BiocInstaller::biocLite("mzR").For the error, seems that proteowizard has problems reading this file. Can you please try the second part, i.e. with
openMSfileand thebackend = "Ramp"option?