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Exporting to mzML #145
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Indeed - pretty cryptic. Could you please disable parallel processing first by setting |
Unfortunatly no less crytic...
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OK, indeed not very helpful - could you eventually provide an example file so that I can reproduce locally? |
I sent an email to johannes.rainer@eurac.edu with a google drive link with 2 ion mobility datasets. Let me know if you got it? |
Did not get any email yet... |
Nothing with the subject line "ion mobility package"? |
Sorry, yes, sure - I found the mail now. And |
No worries, yes neither of them work. |
I finally had time to look into the files. I checked the file "2017121001.mzML". The problem with that is that I've got spectra in there without any peaks. Could you please check this also for your files from above? sum(lengths(exampleIonMob1) == 0) If that's the case I have to think how we're going to handle that. |
- Support export of emtpy spectra with `MsBackendMzR` - tentative fix for issue #145.
- Fix export of empty spectra with `MsBackendMzR` (issue #145).
Note: I've fixed the empty spectra bug in both the BioC 3.12 release branch and the current development (master/main) branch. Could you please install any of the two to see if it fixes your problem @ococrook (e.g. with |
Great, thank you so much. I'll have a check later |
Hi @jorainer, managed to get around to check and looks good to me! My local versions exported correctly. Indeed, there are empty spectra - about 6025/25000 were empty. Just to confirm, if we have Hdf5 backend, we first convert to mzR backend to export. Happy to close the issue. |
If you have a Hdf5 backend you can call |
I'm trying to export a spectra object with backend MsBackendMzR() to a mzML file as given by the example in the vignette. However, I get an error which is a bit cryptic. Sorry Johannes I'm no trying to break everying on purpose ....
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