Can't assign 4 names to a 0 column data.table MSStats errror

[nf-core]

Can't assign 4 names to a 0 column data.table MSStats errror

[jpfeuffer]

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 check this during validation, warn and maybe disable msstats automatically then.
Or only use the normalization or imputation functions in msstats that do not need multiple fractions in such a case.

[YoujiaMa]

@Kimmiecc19 i also meet the same error. u can try set tow or more Condition. MSstats seem to compare different type of data.

[Kimmiecc19]

Hmm... I did try and add two conditions and it still didn't work for some the same reason. I even tried to just keep the sdrf file exactly the same with all samples and conditions and I still got the same error.

Also, is there an issue with using OpenMS files as input? It wouldn't allow me to and said I need to use sdrf instead. I, however, can't recall the exact error right now.

[Kimmiecc19]

It would be great if the pipeline would still run and output results with just one condition but I know that's ultimately not the purpose of the pipeline. Is there a minimum number of each condition that I need? For example three of each? Available data is always so limited.

[simone-pignotti]

I am also running into the same error with quantms v1.2.0. Indeed, checking this during validation and adding an informative error message would be great.