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3.9 years ago

137737756
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I plan to use the DESeq2::rlog transformed TCGA HTseq_counts data and the TCGA clinical data to do survival analysis. But I am confused how to do many genes(>10000) survival analysis at the same time.

I would be grateful if you could give insights.

Thank you!!

Try to do it for one gene, then wrap it in a loop?

To follow on from that, you may consider just looping over the formula for Cox proportional hazards to see which genes are statistically significant from that (and then plotting the curves for those). the Cox proportional hazards model is implemented via

`coxph`

in R: A: cox proportional hazard model