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Meeting 12/16/2019 - Notes #90

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gwaybio opened this issue Dec 16, 2019 · 0 comments
Closed

Meeting 12/16/2019 - Notes #90

gwaybio opened this issue Dec 16, 2019 · 0 comments
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Discussion and Notes Documenting ideas/discussions

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@gwaybio
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gwaybio commented Dec 16, 2019

  • Genes have annotations to function relating to specific cell health phenotypes (Investigate specific CRISPR genes #53 (comment))
  • There are RNAseq data for this perturbations too. Can we compare predictive performance? Maybe certain cell health models are better with either datatype? What about combined?
  • ES2 Cell Line has superior performance in CRISPR experiments. It has high CAS9 expression and behaves nicely (Is there anything remarkable about ES2 cell line compared to A549 and HCT116? #80 (comment))
  • There may be room for various improvements in model building
    • Adjust for single cell penetrance (only build profiles with cells with infections)
    • There may be a copy number effect here for CRISPR knockouts. Could adjust scores by some sort of copy number effect.
  • Perform leave one cell out experiments - this will tell us how well models might generalize to new cell lines.
  • Perform CCA on X and Y matrices and look at loadings to determine clearly, which cell painting features are aligned with cell health phenotypes
@gwaybio gwaybio added the Discussion and Notes Documenting ideas/discussions label Dec 16, 2019
@gwaybio gwaybio closed this as completed Nov 30, 2020
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