Question: Kaplan Meier curves in R
1
gravatar for Palgrave
3.4 years ago by
Palgrave20
Singapore
Palgrave20 wrote:

Hi all,

 

I have gene-expression data of 80 cancer patients coupled with survival data for the same patients. What is the most robust way to calculate and plot survival curves for all my genes using the survival data?

Basically I would like to find those genes whose expression significantly affects survival.

survival rna-seq R • 2.7k views
ADD COMMENTlink modified 3.4 years ago by Alastair Kerr5.2k • written 3.4 years ago by Palgrave20
0
gravatar for Alastair Kerr
3.4 years ago by
Alastair Kerr5.2k
The University of Edinburgh, UK
Alastair Kerr5.2k wrote:

The survival package in R is what I have used in the past.  [This site](http://www.uni-kiel.de/psychologie/rexrepos/posts/survivalKM.html) has a good overview of plotting the curves and [this site](http://www.openintro.org/stat/down/Survival-Analysis-in-R.pdf) has more detail.

I have only done that analysis with WT vs mutant mice, i.e. 1 gene in approx states.  Unless you have some extreme effects in particular genes you may  struggle to get the statistical power needed if you are examining multiple genes in multiple states over a fairly small cohort 

 

 

ADD COMMENTlink written 3.4 years ago by Alastair Kerr5.2k

These are miRNA expression data and it seems to be some effects allready.
 

ADD REPLYlink written 3.4 years ago by Palgrave20
1

How did you determine the cutoff value for the expression data?

ADD REPLYlink written 3.4 years ago by XD10
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