Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Could use a better error message when user requests a bad featureSubset #96

Open
bpolacco opened this issue Apr 4, 2023 · 0 comments
Open

Comments

@bpolacco
Copy link

bpolacco commented Apr 4, 2023

Hello!

Came across this small issue today while running the following code:

dpout.highQuality <- MSstats::dataProcess(frag.mss,
                                          MBimpute = FALSE,
                                          featureSubset = "hiqhQuality",  # <== typo hidden here; q vs g
                                          remove_uninformative_feature_outlier = TRUE)

Error message is:
Error in getOption("MSstatsLog")("INFO", msg) : object 'msg' not found

It was rather puzzling, and made me think a recent MSstats update had broken something. But notice the typo I made for featureSubset. It looks like when an unexpected value is given for featureSubset, the code tries to write a log message that is not yet initialized. I'm guessing the issue is in MSstatsSelectFeatures , where a fall back else {stop ("Unexpected featureSubset value, allowed values are highQuality, ...")}, would be an easy improvement and would have let me find my error much faster.

Thanks!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant