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### Description of the bug
Hi,
I'm trying to run a minimal experiment to test using the SDRF format to develop a TMT pipeline. I've tried copying the format as best I can, but I don't understand w…
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## Bug report
(Please follow this template replacing the text between parentheses with the requested information)
### Expected behavior and actual behavior
When running a pipeline (in this i…
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In the following issue #671 we discussed the major changes for SDRF specification during the next release 1.1. One of them, is the extension of SDRF for metabolomics.
> **GOAL**: The aim of adapti…
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To my understanding, a factor value column should have a corresponding characteristics column. However, when I run the parse_sdrf validate-sdrf command, despite having a factor value column which has …
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suspension: Nucleus vs Cell
ethnicity: Probably not present
donor id: should be in SDRF
is_primary_data: Probably not present
tissue_type: tissue/organoid/cell culture
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It would be great is compareMS2 could infer parameters and input files from an SDRF file. It does not appear to be very difficult. See attached example, corresponding to Figure 3 in the compareMS2 2.0…
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I always use the same SDRF temple. 2024-4-4 it worked, no error, but today it said 'Value is not match with ontology'. I can't tell what is wrong here. I am using px-submission 2.7.3
Here is the file…
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We should have a prototype of an SDRF definition for metabolomics data. EPMA will work with SDRF for the standard metadata for samples for proteomics and metabolomics, and in principle, the file forma…
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Hey,
I noticed the SDRF validator is a bit difficult to maintain and to understand in it's current state, as it is one long python script.
To make it more maintainable and extendable for future c…
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Hi All,
related to the PXD022713 dataset I submitted last week (private for the moment), I encountered a problem with the SDRF file I tried for the first time to generate and submit (as suggested b…
ovigy updated
2 years ago