sneumann/mzR

.mzData.xml files from Agilent parsing

Opened this issue · 2 comments

flomehl commented

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

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
hechth commented

@sneumann do you think it would be possible to provide the mzData functionality as some form of addon? Or do you know about some other package that can read mzData files?