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broadinstitute / cytominer_scripts

Scripts for processing morphological profiling data using cytominer
MIT License
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Confusing Error in `preselect.R` #26

Closed gwaybio closed 5 years ago

gwaybio commented 5 years ago

I am performing a replicate_correlation variable selection with preselect.R.

The error I receive is:

INFO [2019-05-17 15:44:25] Subsetting using Metadata_Well != 'dummy'
INFO [2019-05-17 15:44:25] Performing replicate_correlation...
Joining, by = c("Metadata_Plate_Map_Name", "Metadata_Well")
Error in grouped_df_impl(data, unname(vars), drop) :
  Column `variable` is unknown
Calls: %>% ... group_by.data.frame -> grouped_df -> grouped_df_impl -> .Call
Execution halted

I believe the error is generated in this call to cytominer::replicate_correlation

In cytominer::replicate_correlation, perhaps the error is happening here. Either way, this is something that I need to look into and fix.

gwaybio commented 5 years ago

Turns out that this is the error that is thrown when we do not have replicate plates! When there is only one replicate, or when replicates are included on the same plate, preselect.R will fail with condition="replicate_correlation".