Error in valid object

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Nivedita Bhattacharya

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Jul 24, 2021, 8:30:02 AM7/24/21
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Hi Kylie,

Am getting an error like shown below, what does it mean and how to resolve it?

Error in validObject(x):
   invalid class "atoms" object: 'offset' contains negative indices

Best,
Nivedita

kbemis

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Jul 26, 2021, 3:21:17 PM7/26/21
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This is either an error from an older version of 'matter' (that should be fixed on all recent versions) when reading larger imzML/ibd files, or it indicates that the imzML file may have been improperly written. First, check that you are on a current version of Cardinal/matter; if you are, then try running the imzML file through imzMLValidator (https://gitlab.com/imzML/imzMLValidator) to see if the issues are in the file itself.

-Kylie

Nivedita Bhattacharya

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Jul 27, 2021, 6:50:32 AM7/27/21
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Thank you Kylie for the response, I will run my file through imzMLValidator and get back to you.

Pia Hönscheid

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Oct 28, 2022, 7:52:02 AM10/28/22
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Dear Kylie,
can you give us some update about the issue :

Error in validObject(x):
   invalid class "atoms" object: 'offset' contains negative indices
as we are running into this error using the newest versions of cardinal/r by now (having data sets over 2.5 GB)...

Does the imzmlValidator is still the way to go? Additionally the newest version of validator does not work for us as well as it took ages to calculate all errors...
We would be happy to get some ideas how to improve...

Best& Thank you!
Pia
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