CellProfiler
Add switch to properties file to exclude zero variance features
Does this interfere with any functionality (e.g. classification) or is it just a nuisance? @holgerhennig Closing for now, might add Future consideration label if warranted based on your reply.
@holgerhennig You can analyze all zero variance features using Advanced->Check features. Then either drop those features manually in the properties file or use the normalization tool to delete them.
Thanks @daviddao, that's very helpful! The normalization tool sounds like a good option then to delete zero variance features. Dropping the zero variance features manually in the prop file might be a good option for some users too, but can be more cumbersome. Suggest to add your description above and @AnneCarpenter's decription for the normalization tool in issue #198 to the CPA manual, something like "normalization tool" and "how to delete zero variance features".
@holgerhennig Could you please write that documentation? @N3llz could add it to the CPA manual website once ready.
@AnneCarpenter and @N3llz: Done :) I've forked the CPA manual, updated the CPA manual and filed a pull request. I added section on data preparation (normalization of features, removing zero variance features). Pull request is here: https://github.com/daviddao/CPA-docs/pull/1 Let me know if there's anything else I can do
Awesome thanks so much! The current maintained version is inside CPA itself (https://github.com/CellProfiler/CellProfiler-Analyst/tree/master/docs) , please forget CPA-docs. It's depricated, sry for this! I will just import your change into CPA if you don't mind :)