Julianus Pfeuffer
Julianus Pfeuffer
Are there tests for the graph "module"?
Hmm yes true, maybe it's because of the fact that you only have one condition in your design. MSstats is *mostly* used to find significant proteins between conditions. We should...
Yes, correct. However, this would need to be done inside ProteomicsLFQ. So you would need to raise an issue at OpenMS and link it here.
I think it would be better if openms just exports a fraction column correctly. Instead of hoping for a correct guess b Msstats.
@timosachsenberg I have no idea why this is not the case. I thought we export everything.
I also did a PR to MSstats once to address this issue. Maybe it did not make it into 3.22? Did you check 3.22.1 or whatever ele came before 4?...
https://github.com/Vitek-Lab/MSstats/commit/d78e2aadb6732d363a04503b76dc2297384c30c9
Can you find out why it is not compatible? In theory the openms::openms2.7.0pre package should be built with the latest conda packages. 2.6.0 from bioconda is of course outdated. It...
I would try "mamba" to find the conflicts. Conda is basically useless for this. And in this case even seems to be bugged. I think you can just install mamba...
Why does it want an mqpar.xml at all? We input mztab.