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This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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Chromatograms in row 1 have different mz #511

Open antonwnk opened 3 years ago

antonwnk commented 3 years ago

I get an error when trying to get the chromatograms (a call to the chromatogram function) of an XCMSnExp object with feature definitions present.

Traceback.

``` Error in .mz_chromatograms(object, mz = "mz"): Chromatograms in row 1 have different mz Traceback: 1. chromatogram(a2def_acetone) 2. chromatogram(a2def_acetone) 3. .local(object, ...) 4. lapply(seq_len(nrow(res)), function(r) { . fdev <- featureDefinitions(object, mz = mz(res)[r, ], rt = rt) . if (nrow(fdev)) { . fdev$row <- r . .subset_features_on_chrom_peaks(fdev, chromPeaks(object), . pks_sub) . } . else DataFrame() . }) 5. FUN(X[[i]], ...) 6. featureDefinitions(object, mz = mz(res)[r, ], rt = rt) 7. featureDefinitions(object, mz = mz(res)[r, ], rt = rt) 8. .local(object, ...) 9. mz(res) 10. mz(res) 11. .local(object, ...) 12. .mz_chromatograms(object, mz = "mz") 13. stop("Chromatograms in row ", i, " have different ", mz) ```

My XCMSnExp object, `a2def_acetone`: a set of "full-size" GC-MS samples `filterRt`-ed to where we expect to find acetone.

``` > a2def_acetone MSn experiment data ("XCMSnExp") Object size in memory: 10.31 Mb - - - Spectra data - - - MS level(s): 1 Number of spectra: 29324 MSn retention times: 4:5 - 4:56 minutes - - - Processing information - - - Data loaded [Fri Sep 25 21:11:00 2020] Filter: select MS level(s) 1 [Fri Sep 25 21:11:08 2020] Filter: select retention time [70-1400] and MS level(s), 1 [Fri Sep 25 21:11:08 2020] Filter: trim MZ [35..250] on MS level(s) 1. Spectra of MS level(s) 1, cleaned: Fri Sep 25 21:11:08 2020 Removed 1208 empty spectra. [Fri Sep 25 21:16:04 2020] Filter: select retention time [245-296] and MS level(s), 1 [Wed Sep 30 09:24:53 2020] MSnbase version: 2.12.0 - - - Lazy processing queue content - - - o filterMz o clean - - - Meta data - - - phenoData rowNames: AS-021B-0-1139480.mzML AS-021B-1-1124475.mzML ... VIW-6-1-1139346.mzML (115 total) varLabels: sampleNames varMetadata: labelDescription Loaded from: [1] AS-021B-0-1139480.mzML... [115] VIW-6-1-1139346.mzML Use 'fileNames(.)' to see all files. protocolData: none featureData featureNames: F001.S1240 F001.S1241 ... F115.S1478 (29324 total) fvarLabels: fileIdx spIdx ... spectrum (35 total) fvarMetadata: labelDescription experimentData: use 'experimentData(object)' - - - xcms preprocessing - - - Chromatographic peak detection: unknown method. 6278 peaks identified in 115 samples. On average 54.6 chromatographic peaks per sample. Correspondence: method: chromatographic peak density 128 features identified. Median mz range of features: 0.055494 Median rt range of features: 8.7451 ```

Trying to figure out what was going on I debugged the failing MSnbase:::.mz_chromatograms call and saw that the returned mz ranges have as lower bound the actual minimum mz found in the sample (as per filterFile(xcmsObj, n) %>% mz %>% unlist(use.names = FALSE) %>% min).

Browse[2]> rngs <- unique(do.call(rbind, lapply(x@.Data[i, ], getMethod(mz, "Chromatogram"))))
Browse[2]> rngs                                                                                                                                                               
                              [,1] [,2]
AS-021B-0-1139480.mzML    35.56396  250
AS-021B-1-1124475.mzML    35.56592  250
AS-023-0-1028176.mzML     35.56171  250
AS-023-1-1030346.mzML     35.56258  250
AS-024-0-11261-38.mzML    35.55937  250
[...]

Finally, another thing that I observed, which I don't know if is relevant. I have 2 objects (both fail the same way when trying to use chromatogram(.)):

The numbers from the rngs variable in the debugger output correspond to the minimum mz values of the a2def object, rather than the minimum mz values in the a2def_acetone variable which was passed to the chromatogram function when debugging.

Thanks for the read and let me know what you think.

Edit: Realized I am using a quite outdated XCMS version: 3.8.2

`sessionInfo()`

``` R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] xcms_3.8.2 MSnbase_2.12.0 ProtGenerics_1.18.0 [4] S4Vectors_0.24.4 mzR_2.20.0 Rcpp_1.0.5 [7] BiocParallel_1.20.1 Biobase_2.46.0 BiocGenerics_0.32.0 [10] RColorBrewer_1.1-2 lattice_0.20-41 ggplot2_3.3.2 [13] stringr_1.4.0 purrr_0.3.4 dplyr_1.0.1 [16] magrittr_1.5 loaded via a namespace (and not attached): [1] digest_0.6.25 foreach_1.5.0 IRdisplay_0.7.0 [4] R6_2.4.1 plyr_1.8.6 repr_1.1.0 [7] mzID_1.24.0 evaluate_0.14 pillar_1.4.6 [10] zlibbioc_1.32.0 rlang_0.4.7 uuid_0.1-4 [13] Matrix_1.2-18 preprocessCore_1.48.0 splines_3.6.0 [16] munsell_0.5.0 compiler_3.6.0 pkgconfig_2.0.3 [19] base64enc_0.1-3 multtest_2.42.0 pcaMethods_1.78.0 [22] htmltools_0.5.0 tidyselect_1.1.0 tibble_3.0.3 [25] RANN_2.6.1 IRanges_2.20.2 codetools_0.2-16 [28] XML_3.99-0.3 crayon_1.3.4 withr_2.2.0 [31] MASS_7.3-51.6 MassSpecWavelet_1.52.0 grid_3.6.0 [34] jsonlite_1.7.0 gtable_0.3.0 lifecycle_0.2.0 [37] affy_1.64.0 scales_1.1.1 ncdf4_1.17 [40] stringi_1.4.6 impute_1.60.0 affyio_1.56.0 [43] doParallel_1.0.15 limma_3.42.2 robustbase_0.93-6 [46] ellipsis_0.3.1 generics_0.0.2 vctrs_0.3.2 [49] IRkernel_1.1.1 iterators_1.0.12 tools_3.6.0 [52] glue_1.4.1 DEoptimR_1.0-8 survival_3.2-3 [55] colorspace_1.4-1 BiocManager_1.30.10 vsn_3.54.0 [58] MALDIquant_1.19.3 pbdZMQ_0.3-3 ```

jorainer commented 3 years ago

Uh, this is a really old version of xcms. Could you please check if you get the same error with the current version of xcms (3.10.2)?

antonwnk commented 3 years ago

I managed to update my environment but I seem to get the same error.

Traceback

``` > b = chromatogram(a, aggregationFun = "sum") Error in .mz_chromatograms(object, mz = "mz") : Chromatograms in row 1 have different mz 13: stop("Chromatograms in row ", i, " have different ", mz) 12: .mz_chromatograms(object, mz = "mz") 11: .local(object, ...) 10: mz(res) 9: mz(res) 8: .local(object, ...) 7: featureDefinitions(object, mz = mz(res)[r, ], rt = rt) 6: featureDefinitions(object, mz = mz(res)[r, ], rt = rt) 5: FUN(X[[i]], ...) 4: lapply(seq_len(nrow(res)), function(r) { fdev <- featureDefinitions(object, mz = mz(res)[r, ], rt = rt) if (nrow(fdev)) { fdev$row <- r .subset_features_on_chrom_peaks(fdev, chromPeaks(object), pks_sub) } else DataFrame() }) 3: .local(object, ...) 2: chromatogram(a, aggregationFun = "sum") 1: chromatogram(a, aggregationFun = "sum") ```

sessionInfo()

``` R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS: /rwthfs/rz/SW/R/R-4.0.2/lib64/R/lib/libRblas.so LAPACK: /rwthfs/rz/SW/R/R-4.0.2/lib64/R/lib/libRlapack.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C 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_0.26.1 mzR_2.22.0 Rcpp_1.0.5 [7] BiocParallel_1.22.0 Biobase_2.48.0 BiocGenerics_0.34.0 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_1.4-1 vctrs_0.3.4 [7] generics_0.0.2 vsn_3.56.0 [9] XML_3.99-0.5 rlang_0.4.7 [11] pillar_1.4.6 glue_1.4.2 [13] affy_1.66.0 RColorBrewer_1.1-2 [15] matrixStats_0.57.0 affyio_1.58.0 [17] GenomeInfoDbData_1.2.3 foreach_1.5.0 [19] lifecycle_0.2.0 plyr_1.8.6 [21] mzID_1.26.0 robustbase_0.93-6 [23] zlibbioc_1.34.0 munsell_0.5.0 [25] pcaMethods_1.80.0 gtable_0.3.0 [27] codetools_0.2-16 IRanges_2.22.2 [29] doParallel_1.0.15 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_0.28.0 [39] RANN_2.6.1 impute_1.62.0 [41] ggplot2_3.3.2 digest_0.6.25 [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_3.0.3 crayon_1.3.4 [53] pkgconfig_2.0.3 Matrix_1.2-18 [55] MASS_7.3-51.6 ellipsis_0.3.1 [57] iterators_1.0.12 R6_2.4.1 [59] MALDIquant_1.19.3 compiler_4.0.2 ```

jorainer commented 3 years ago

Hm, strange. Could you eventually provide one or two files (or a subset of that) for which this happens so that I could check that locally and fix?

RemyDeB commented 1 year ago

Hi, this is an old topic but i got the same error. This occure when i try to apply filterRt before chromatogram function. If i use chromatogram first them filterRt , it's work. Hope this can help people. Regards, Remy

jorainer commented 1 year ago

I'm working on a fix... thanks for reporting/reminding