Missing `broad_sample` IDs in ORF and CRISPR platemap files

[jenna-tomkinson]

Problem

When connecting the plate map files and metadata files, we find that there are missing broad_sample IDs in all plate maps, causing single cells to have no metadata (when processing with pycytominer).

When looking at the documentation in the main README, we find that there are 4 "empty" wells from each of these experiments:

But, the term empty is not defined. We had assumed it meant there were no cells so the well is empty. But, we find that plates from these experiments do infact contain single cells as morphology features were extracted.

Question

@gwaybio let us know that this probably indicates not that the well is empty of cell, but is empty of treatment.

Can you confirm that this is correct and empty is synonymous with no treatment?

If so, we would be able to get around the missing metadata issue by including a fake broad_sample ID to these wells so that the single cell data is not removed during processing.

[niranjchandrasekaran]

Hi @jenna-tomkinson, your understanding is correct. empty is synonymous with no treatment in the ORF and CRISPR platemaps. Using a fake ID is a good workaround.

[jenna-tomkinson]

@niranjchandrasekaran

Thank you so much for the confirmation!