.mzData.xml files from Agilent parsing

sneumann / mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

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.mzData.xml files from Agilent parsing #294

Open flomehl opened 2 months ago

flomehl commented 2 months ago

Hi, I wish to parse .mzData.xml files from Agilent to extract a RT x m/z matrix, I've correctly installed the mzR package but I obtain this issue: Error in .mzRBackendFromContent(x) : Could not determine file type for mZdata/120_copy.mzData.xml Do you by chance have an idea about where this issue could come? thanks a lot, Florence

sneumann commented 2 months ago

Hi, parsing of mzData files has been removed a while ago in version mzR-2.29.3. Your two choices are 0) Convert from Agilent to mzML (which is the recommended open data format) 1) Manually install an older mzR version that still supports mzData (older than 2.29.3) 2) Use the OpenMS FileConverter tool to convert to the mzData to mzML. Yours, Steffen