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broadinstitute / profiling-resistance-mechanisms

Predicting pharmacodynamic responses to cancer drugs using cell morphology
BSD 3-Clause "New" or "Revised" License
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Bortezomib signature platemap effect? #98

Closed gwaybio closed 3 years ago

gwaybio commented 3 years ago

Confirm that platemap is not influencing the signature we observed in #94

AnneCarpenter commented 3 years ago

A simple visualization of the different samples across plates/batches would do!

gwaybio commented 3 years ago

Based on quick visualizations, there do not appear to be any strong plate position effects for all plates:

Here is the holdout plate:

Signature scores

2021_03_03_Batch14_219901_signature_plate_effect

Full plate layout

2021_03_03_Batch14219901_plate_effects_replicates

gwaybio commented 3 years ago

Figures for all 7 plates are here: https://github.com/broadinstitute/profiling-resistance-mechanisms/tree/9feaa87880f332ef2532cd7aada893927a8c0888/3.resistance-signature/figures/plate_effects

AnneCarpenter commented 3 years ago

Super, I was looking mainly for bad plate layout rather than bad plate effects now that I think of it, and these visualizations effectively show there is nothing fishy going on for either (also that Batches 15 onwards look pretty great!) @gwaygenomics