benchmark L1000 similarity measures across cell lines

[alexvpickering]

samuelfinlayson suggested assessing similarity measures like in my previous blog post but instead of using external GEO datasets, using LINCS data from one cell line to try and retrieve the same perturbation in a different cell line.

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This approach has some nice advantages:

• no need to gather/label external data
• creates a larger training dataset for possible neural networks

[alexvpickering]

➤ Samuel Finlayson commented:

Let's go ahead and tentatively assign this to me and Maria (the Masters student) for now, with your involvement to any extent you desire, of course. I think it is low priority from the "minimum viable product" perspective, but could make for a decent paper, so could be good thesis fodder for Maria.

[alexvpickering]

samuelfinlayson Sounds good. Just setting down some notes on things that we discussed today. Please clarify/comment if I got anything mixed up on any of the other cards.