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zhangxiaoyu11 / OmiEmbed

Multi-task deep learning framework for multi-omics data analysis
MIT License
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survival analysis #3

Open Hchang77 opened 2 years ago

Hchang77 commented 2 years ago

Hello My major field is medicine and I am new to python code.

I try to analyze the RNA-seq and survival data with OmiEmbed. RNA-seq data (A.tsv) and survival data (survival.tsv) are located in 'data' folder, respectively. I ran train_test.py, but the result was 'FileNotFoundError: [Errno 2] No such file or directory: './data/labels.tsv'

What arguments are needed for survival analysis using one RNA-seq data and one survival data?

Best regards,

wmrenr commented 2 years ago

There are labels in my file.

Hchang77 commented 2 years ago

Thanks for your reply.

I understand that RNA-seq data (A.tsv), survival data (survival.tsv) and labels (labels.tsv) are needed for survival analysis.

What information does 'labels.tsv' contain? Event of survival was already included in survival.tsv (Death = 1, alive = 0)

Regards,

wmrenr commented 2 years ago

No,the labels contain sample and samp[le_type.samples ,for exsample ,the first row is TCGA-WH-A86K-01A , 0.

wmrenr commented 2 years ago

I am also a beginner of pytorch, can you leave a contact information, let's discuss it together？