Preprocessing and Feature Extraction of RNA-seq data

[dddavid4real]

Hi, thank you for this great work!

I'm wondering if you could provide the script or pipeline for pre-processing and feature extraction of genetic files. To be more specific, I notice that you provide .pt files for RNA-seq data. Could you share some info about how to get this .pt file? Thanks again!

[guillaumejaume]

Apologies for the very late reply. We followed a strategy similar to https://github.com/mahmoodlab/MMP/blob/main/src/preprocess_pancancer_TCGA_normalized_RNA.ipynb.

Long story short, we took data from the Xena portal, here: https://xenabrowser.net/datapages/

[liujun0621]

Thanks for doing a great job! transciptomics pt file shape [4999,1] What gene does each row correspond to?

[liujun0621]

[MichealgodJordan]

Apologies for the very late reply. We followed a strategy similar to https://github.com/mahmoodlab/MMP/blob/main/src/preprocess_pancancer_TCGA_normalized_RNA.ipynb.

Long story short, we took data from the Xena portal, here: https://xenabrowser.net/datapages/

Could you please share the method you obtain the RNA .pt files? I saw this preprocessing method to obtain a CSV file, but I have no idea about how to extract its features into .pt files in your way. Could you please provide code or examples? Thanks.