cox PH model - KM curve
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@adrian-johnson-2728
Last seen 3.9 years ago
Dear group: I have gene expression data matrix (after RMA) as a matrix. In another table (as data frame) I have survival data. I have 25 genes for which I want to plot a Kaplan-meier curves based on cox model for these 25 genes. Is there a workflow to do this analysis. I tried phenoTest, however I do not know how to make use of heatmapPhenoTest function on a given gene. I appreciate your help. Thanks Adrian.
Survival phenoTest Survival phenoTest • 1.2k views
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Heidi Dvinge ★ 2.0k
@heidi-dvinge-2195
Last seen 9.5 years ago
Hi Adrian, have you tried playing with the "survival" package? Functions such as Surv(), coxph() and survfit() could probably help you do what you're after. HTH \Heidi > Dear group: > I have gene expression data matrix (after RMA) as a matrix. In another > table (as data frame) I have survival data. I have 25 genes for which > I want to plot a Kaplan-meier curves based on cox model for these 25 > genes. Is there a workflow to do this analysis. > I tried phenoTest, however I do not know how to make use of > heatmapPhenoTest function on a given gene. > > I appreciate your help. Thanks > Adrian. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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