greenelab / BioBombe

BioBombe: Sequentially compressed gene expression features enhances biological signatures
https://greenelab.github.io/BioBombe/
BSD 3-Clause "New" or "Revised" License
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Adding NBL Cell Line T-Test Results #173

Closed gwaybio closed 5 years ago

gwaybio commented 5 years ago

do you tend to put the year that a script was created or when it was last updated?

I typically sign my name and date upon script creation. However, since github tracks these types of things you can easily see contributions (when and who), so it doesn't really matter.

I wonder if you might want to add additional details in your function for "apply_signature" or add a comment where you all this function because I'm not exactly sure if i'm understanding the output correctly.

Yeah, that sounds like a good idea. I added documentation to the function definition.

Based on the function call it looks like you're returning the vae_111 feature of your nbl_df but I'm not sure how you got this.

Yep! In the function i specify top_feature (which stores the string vae_111). Basically I multiply nbl_df by the compressed feature vae_111

When you are retrieving the weight matrix, I was expecting to see vae features, instead there are pca features. Is this correct?

Yeah, the data structure decision I made early on was to save all weight matrices (within a specific k) in the same matrix. So that weight matrix has PCA, ICA, NMF, DAE, and VAE features.