Can’t generate NEPDF data for the example sc-RNA seq data

[Jiang Feng]

Hello!
I have a new problem: The get_xy_label_data_cnn_combine_from_database.py report an error when generate NEPDF data for the example sc-RNA seq h5 file
python CNNC/get_xy_label_data_cnn_combine_from_database.py \ None \ CNNC/data/sc_gene_list.txt \ CNNC/data/dendritic_gene_pairs_200.txt \ CNNC/data/dendritic_gene_pairs_200_num.txt \ None \ CNNC/Data_sources/dendritic_cell.h5 \ 1. The dendritic_cell.h5 was downloaded from

Then it reported errors:

So I opened the h5 file by h5py and changed the key from "RPKMs" to "rpkm". However, it also reported errors:

It works well when I run this command for the bulk RNA seq data "mouse_bulk.h5", so I wonder if the sc-RNA seq data should be different from bulk data or some other reasons?
Tanks a lot!

[xiaoyeye]

Hi,
It seems that the problem lies in the store function. I wonder what if you change to rpkm = store['RPKMs']?
Best

[Jiang Feng]

I edited the "get_xy_label_data_cnn_combine_from_database.py", then it runs well on example sc-RNA seq data.
However, when I use it to run on my own sc-RNA seq data, it reported the same error:

The sc-RNA seq .h5 file was generate from my own expression matrix with h5py module, and have the same structure with the example .h5 file.

[xiaoyeye]

Well. It is hard for me to debug based on other datasets. Generally speaking, the "store" function is used to read the expression data as a pd.DataFrame format, so I believe any function that is able to achieve this can be used. Of course, please pay attention to its columns name which is gene symbol. hope it can help.

[Jiang Feng]

Thanks!
I generate the h5 file with pd.HDFStore and it runs well.
Another question is about the get_xy_label_data_cnn_combine_from_database.py scripts:

I noticed the annotation and removed the "[0:43261]" as described, and I already know the 43261 means the number of samples in the sc data. However, I also noticed the "43261" with green box marked (130 and 136 lines) . So should I modify this number with my own sc-RNA data samples counts?

[xiaoyeye]

Great!

Yes, you can modify this number with your own data.
Best