Error in writeMSData

[lshyun0415]

Hello, I'm trying to export my preprocessed XCMSnExp object (neighboring peak merged, RT aligned, feature grouped, gap filled) as individual mzml files by sample, but it's been giving a subscript out of bounds error. I wasn't sure where the problem was coming from since I used a character vector of the sample names as input for the file parameter. I tried subsetting the XCMSnExp object by sample and saving it individually, but it still gave me the same error message.

Also, is there a way to save the entire XCMSnExp object as an mgf or msp file?

I attached my code and the error message below. Any comment would help. Thank you so much!

**XCMSnExp object
show(xchr_ftgr)
MSn experiment data ("XCMSnExp")
Object size in memory: 19.49 Mb

• • • Spectra data - - -
      MS level(s): 1 2
      Number of spectra: 58188
      MSn retention times: -1:48 - 16:04 minutes
• • • Processing information - - -
      Data loaded [Wed Sep 13 16:21:20 2023]
      MSnbase version: 2.26.0
• • • Meta data - - -
      phenoData
      rowNames: 1 2 ... 34 (34 total)
      varLabels: sample_name sample_group
      varMetadata: labelDescription
      Loaded from:
      [1] 230810_NO68_M7_C_1-1_P.mzML... [34] 230810_NO101_M7_D_8-4_8-5_P.mzML
      Use 'fileNames(.)' to see all files.
      protocolData: none
      featureData
      featureNames: F01.S0001 F01.S0002 ... F34.S1630 (58188 total)
      fvarLabels: fileIdx spIdx ... spectrum (35 total)
      fvarMetadata: labelDescription
      experimentData: use 'experimentData(object)'
• • • xcms preprocessing - - -
      Chromatographic peak detection:
      method: centWave
      901440 peaks identified in 34 samples.
      On average 26513 chromatographic peaks per sample.
      Alignment/retention time adjustment:
      method: obiwarp
      Correspondence:
      method: chromatographic peak density
      8786 features identified.
      Median mz range of features: 0.0032953
      Median rt range of features: 29.115
      106999 filled peaks (on average 3147.029 per sample).

**Export code
xcms::writeMSData(object = xchr_ftgr,
file = basename(phenoData(xchr_filled)$sample_name)[1],
outformat = "mzml",
copy = T)

**Error message
Error in (function (cond) :
error in evaluating the argument 'args' in selecting a method for function 'do.call': subscript out of bounds

[sneumann]

Hi, thanks for reporting. Is there a way you can reproduce this with the faahKO data ? If so, we could include this as test case and fix what's broken. Or is that specific to your data set ? Can you give us some debugging information, e.g. versions (xcms and MSnbase) and either use the debugger to check what's wrong, or if you are not a seasoned R hacker (yet), then after the error occurs the output of the traceback() command ?

Yours,
Steffeb