If you mix up the channel order in the sampletable (even when keeping mappings to sample names and groups correct), the "design" for the linear model will follow the mix-up. As the channel order of the quant matrix will not change, they will be misaligned. This will give incorrect channels per sample group and thus wrong DEqMS output (logFC etc). Documenting this here, fix coming soon.
If you mix up the channel order in the sampletable (even when keeping mappings to sample names and groups correct), the "design" for the linear model will follow the mix-up. As the channel order of the quant matrix will not change, they will be misaligned. This will give incorrect channels per sample group and thus wrong DEqMS output (logFC etc). Documenting this here, fix coming soon.
Bug found by @happywing-KI