Cell count variation

[alxndrkalinin]

1. Exploring cell count variability

Due to strong presence of per-batch/plate patterns in cell count (CC) visualizations (#7), we wanted to look if cell count variability has a relationship with position effect retrievability metrics (#9). To do so, we added Metadata_Count_Cells column to metadata (from jump-cellpainting/morphmap@dbbd1c3) and calculated it's coefficient of variation (CoV). We then empirically chose a cutoff value of CoV=0.12 to split ORF into low and high CC variability.

Cell counts	Cell count CoV	Cell counts split @ CoV=0.12

2. Subsetting same ORF, same well mAP based on low vs high cell count variability

Based on low/high variability, we can select ORFs from the subset that we used to calculate mAP for raw and baseline-corrected data (see #9). Due to low number of samples in same ORF, different well and same well, different ORF, it makes sense to look at same ORF, same well. Columns are the same as in #9:

• "subset": a subset of raw uncorrected data
• "subset->correct": a subset of raw profiles that were then corrected by subtracting per-well mean on this subset
• "correct->subset": a subset of corrected profiles, which were corrected by subtracting per-well mean on full data

2.1 Low cell count variability ORFs

Setting	Data	mmAP	Percent retrieved (p<0.05)
same well, same ORF	raw	0.231	0.969 (2519/2600)
same well, same ORF	subset->correct	0.177	0.816 (2121/2600)
same well, same ORF	correct->subset	0.242	0.7 (1821/2600)

Low CC CoV visualization

2.2 High cell count variability ORFs

Setting	Data	mmAP	Percent retrieved (p<0.05)
same well, same ORF	raw	0.113	0.737 (776/1053)
same well, same ORF	subset->correct	0.134	0.674 (710/1053)
same well, same ORF	correct->subset	0.245	0.644 (678/1053)

High CC CoV visualization

Metrics on uncorrected data differ substantially between low and high variability subsets. Per-well mean subtraction reduces this difference.

2.3 All ORFs

For the reference, results for from #9

Setting	Data	mmAP	Percent retrieved (p<0.05)
same well, same ORF	raw	0.197	0.902 (3295/3653)
same well, same ORF	subset->correct	0.165	0.775 (2831/3653)
same well, same ORF	correct->subset	0.243	0.684 (2499/3653)

3. Visualizing distributional relationships between mAP and cell count variability (all ORFs)

Instead of splitting ORFs into low/high variability, we can also plot all their mAPs vs CoVs. There are very few ORFs that have both high cell count variability and mAP values/significance.

mAPs vs CoVs color-coded by p-values

CoVs vs p-values color-coded by mAP values