gwaybio
commented
3 years ago @AdeniyiML - this is beautiful.
I see a couple things from this analysis:
- Cell Painting gets more MOAs "right" and more MOAs "wrong" than L100
- Only a handful of MOAs have really strong groups in L1000
- Dose doesn't really impact things all that much
A couple things to keep in mind:
- we know that MOA annotations are wrong - thinking that they aren't will hurt us trying to interpret these results
- It makes sense to me that morphology will group things more tightly than gene expression. There are many ways to alter a gene expression profile that can manifest into similar morphology.
- I am most interested in following up on some groups of MOAs that are bad in one tech and good in the other (the off-diagonal)👇
AdeboyeML
I am pasting @AdeboyeML's analysis performed in https://github.com/broadinstitute/lincs-profiling-comparison/issues/2#issuecomment-729394257 so that we can continue a targeted discussion in a clean github issue:
@shntnu @gwaygenomics
Comparing the distribution of median scores between L1000 and Lincs Cell painting Consensus datasets
- Major points
213 MOAs (Mechanism of actions) present in both Cell painting and L1000 Level-5 data are compared based on the distribution of their median scores.
During alignment of MOAs in L1000 with the MOAS in Cell painting, I realized that MOAs found in the same broad sample in both L1000 & Cell painting data are partly named differently i.e. the naming of same MOAS in both are not consistent.
Results -- MODZ Consensus dataset
Scatter plot btw L1000 vs Lincs Cell Painting median scores per dose
Distribution of median scores in L1000 and Cell Painting Data per dose
Distribution on a dose-by-dose basis
- I am still trying to figure out the reason behind the relationship between the p-value and median scores (null distribution) in https://github.com/broadinstitute/lincs-profiling-comparison/issues/2#issuecomment-726123235