IMA sample issue

Question

IMA sample issue

v-mahughes opened this issue 10 months ago · 7 comments

I was able to download both files onto my system (green_monkey.h5ad and IMA_sample.h5ad). I could successfully read in green monkey data with scanpys read_h5ad function. However, when I try to read in the ima sample data with scanpy.read_h5ad I get the following error: OSError: Unable to open file (file signature not found)

I have checked to ensure the file size matches the file size on the google drive.

Answer 1 · 2024-02-12T19:19:03.000Z

That error might indicate that the file did not finish downloading properly.

Answer 2 · 2024-02-12T20:55:27.000Z

was able to download fully. In 2d i notice that not all coarse cell type annotations in the IMA lymph sample are included in the figure. Were all coarse cell types of the lymph data included in training / testing? or was the dataset restricted to those shown in the figure

Answer 3 · 2024-02-12T21:15:47.000Z

Also, the ima sample data does Not contain the UCE embeddings (no 'X_uce' layer) , but the green monkey data does.

Answer 4 · 2024-02-12T21:16:42.000Z

Or is the adata.X layer the uce embeddings? seems to be of the correct shape (1280)

Answer 5 · 2024-02-12T22:14:02.000Z

For that file .X is the UCE embeddings

Answer 6 · 2024-02-13T00:14:27.000Z

would it be possible for you to provide the filtered, gene epxression matrix for this dataset as well ?

Answer 7 · 2024-02-13T01:31:19.000Z

Unfortunately we don't have that for this file. Since it's collected from so many datasets, and from many different species, it would be difficult to create a corresponding gene expression dataset.