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garfield320
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@garfield320-18805
Last seen 3.4 years ago
I'm trying to read in a mzXML file to R using the xcms package and I keep on getting this error.
> mzxcms <- xcmsRaw("datafile.mzXML",profstep=0.01,profmethod="bin",profparam=list(),includeMSn=FALSE,mslevel=NULL, scanrange=NULL)
Error in validObject(.Object) :
invalid class “xcmsFileSource” object: superclass "characterORconnection" not defined in the environment of the object's class
I'm not sure if this has to do anything with the warnings I get when I load xcms (I'm getting warning messages that I haven't seen before, and I'm worried if some of the packages I've updated for different things are colliding). These are the warnings I get when I call xcms.
> library(xcms)
Warning messages:
1: package ‘BiocGenerics’ was built under R version 4.0.3
2: package ‘Biobase’ was built under R version 4.0.3
3: In fun(libname, pkgname) :
mzR has been built against a different Rcpp version (1.0.4.6)
than is installed on your system (1.0.5). 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.
4: package ‘S4Vectors’ was built under R version 4.0.3
5: multiple methods tables found for ‘which’
And below is my sessionInfo:
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] xcms_3.10.2 MSnbase_2.14.2 ProtGenerics_1.20.0
[4] S4Vectors_0.28.0 mzR_2.22.0 Rcpp_1.0.5
[7] BiocParallel_1.22.0 Biobase_2.50.0 BiocGenerics_0.36.0
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.18.2 tidyselect_1.1.0
[3] purrr_0.3.4 lattice_0.20-41
[5] colorspace_2.0-0 vctrs_0.3.4
[7] generics_0.1.0 vsn_3.56.0
[9] XML_3.99-0.5 rlang_0.4.8
[11] pillar_1.4.6 glue_1.4.2
[13] affy_1.66.0 RColorBrewer_1.1-2
[15] matrixStats_0.57.0 GenomeInfoDbData_1.2.3
[17] affyio_1.58.0 foreach_1.5.1
[19] lifecycle_0.2.0 plyr_1.8.6
[21] mzID_1.26.0 robustbase_0.93-6
[23] zlibbioc_1.36.0 munsell_0.5.0
[25] pcaMethods_1.80.0 gtable_0.3.0
[27] codetools_0.2-16 IRanges_2.24.0
[29] doParallel_1.0.16 GenomeInfoDb_1.24.2
[31] MassSpecWavelet_1.54.0 preprocessCore_1.50.0
[33] DEoptimR_1.0-8 scales_1.1.1
[35] BiocManager_1.30.10 DelayedArray_0.14.1
[37] limma_3.44.3 XVector_0.30.0
[39] RANN_2.6.1 impute_1.62.0
[41] ggplot2_3.3.2 digest_0.6.27
[43] dplyr_1.0.2 ncdf4_1.17
[45] GenomicRanges_1.40.0 grid_4.0.2
[47] tools_4.0.2 bitops_1.0-6
[49] magrittr_1.5 RCurl_1.98-1.2
[51] tibble_3.0.4 crayon_1.3.4
[53] pkgconfig_2.0.3 MASS_7.3-53
[55] ellipsis_0.3.1 Matrix_1.2-18
[57] rstudioapi_0.12 iterators_1.0.13
[59] R6_2.5.0 MALDIquant_1.19.3
[61] compiler_4.0.2
Can anyone give me suggestions on why I can't read my data files in?
I highly discourage the use of the
xcmsRawfunction or any other function from the original xcms package. We partially rewrote the package to re-use functionality for MS data handling from theMSnbasepackage - and the new functionality is stable and being further developed while I don't fix or update the old code base anymore.I would suggest to use:
to read the raw MS data into R. Please have a look at the package vignette (here) or to the small tutorial on MS data handling and processing with
MSnbaseandxcmshere to get some more information on the new functionality.Hi, I have the same issue. I am trying to read netCDF data converted from Agilent Chemstation .D files. With xcmsRaw(), I got a similar error @garfield320, while using readMSData(), I got the following:
Polarity can not be extracted from netCDF files, please set manually the polarity with the 'polarity' method. Error in readInMemMSData(files, pdata = pdata, msLevel. = msLevel., verbose = verbose, : No MS(n>1) spectra in fileC:\Users\qizhi\Documents\R\win-library\4.0\faahKO\cdf\KO\ko15.CDF
Any idea about how to read netCDF data?
Best regards, Qizhi Su
According to the error message you don't have MS level 2 data in the CDF file. I would suggest to load the data with
readMSData(<file name>, mode = "onDisk")i.e. in on-disk mode, which will also import MS1 and MS2 spectra (if there were any). The in-memory mode reads by default only MS2 data. If you want to read the data with that you need to specify that you want specifically MS1 spectra:readMSData(<file name>, msLevel = 1, mode = "inMem").