efst | Python Encrypted FS tools

 by   akpw Python Version: Current License: Non-SPDX

kandi X-RAY | efst Summary

kandi X-RAY | efst Summary

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Python Encrypted FS tools
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            efst Key Features

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            efst Examples and Code Snippets

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            Community Discussions

            QUESTION

            Getting P-Values of Zero in Cox Regression: R
            Asked 2020-Feb-28 at 03:48

            I am a student conducting a gene expression survival analysis in R. I have the expression data for 249 patients, and I am using 6,000 genes as well as their event-free survival times and vital state as response variables. When I tried to run the Cox regression on my dataset, I got extremely strange results (p-values of 0.00 and strange hazard ratios). I have checked over my code multiple times, but I am not able to catch my mistake (when I tried earlier with just one gene, it worked fine, but when I try to test multiple genes using the '.' function, I am not getting porper results). I would highly appreciate any help and have attached both my code and output! Let me know if more information is needed.

            ...

            ANSWER

            Answered 2020-Feb-25 at 02:40

            Except for the first two coefficients (EFST and Status), the coefficients for all other genes are either extremely small or extremely large, leading to very large negative/positive t-statistics, which explains the p-values you're seeing.

            I'm not exactly sure I understood what you're doing. Wouldn't regressing on 6,000 genes in your 249 patients data mean that you're having way more parameters than observations?

            In which case, you're running into overfitting issues which would explain the parameter estimates.

            Source https://stackoverflow.com/questions/60386233

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