Question: Chromatographic peak detection failed for all files
0
gravatar for yuchiu
15 months ago by
yuchiu0
yuchiu0 wrote:

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     

xcms • 293 views
ADD COMMENTlink modified 15 months ago • written 15 months ago by yuchiu0

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:

library(mzR)
fh <- openMSfile(".//Control/BE-C1.mzXML", backend = "pwiz")
hdr <- mzR::header(fh)
nrow(hdr)
spctr <- mzR::peaks(fh)
length(spctr)
mzR::close(fh)

## Repeat with backend Ramp
fh <- openMSfile(".//Control/BE-C1.mzXML", backend = "Ramp")
hdr <- mzR::header(fh)
nrow(hdr)
spctr <- mzR::peaks(fh)
length(spctr)
mzR::close(fh)

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.

ADD REPLYlink written 15 months ago by Johannes Rainer1.5k

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.

ADD REPLYlink written 15 months ago by yuchiu0

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.

ADD REPLYlink written 15 months ago by yuchiu0

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 openMSfile and the backend = "Ramp" option?

ADD REPLYlink modified 15 months ago • written 15 months ago by Johannes Rainer1.5k
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