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abidlabs / contrastive

Contrastive PCA
MIT License
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Unclear how to format input matrices #2

Closed kieran-mace closed 7 years ago

kieran-mace commented 7 years ago

Not sure what shape the input matrices take, however I'm getting the following issue:

My background matrix has 6000 genes, and 39 conditions (6000X39) My foreground matrix has 6000 genes, and 261 conditions (6000X261)

Running mdl.fit_transform gives me this error: ValueError: operands could not be broadcast together with shapes (261,261) (39,39)

Also, should I normalize my matrices first?

kieran-mace commented 7 years ago

It seems to work if I transpose the two input matrices.