[BioC] microarray data and survival analysis

[Charles C. Berry]

On Tue, 20 Feb 2007, Dr_Gyorffy_Balazs wrote:

> Dear All!
>
>  I have microarray data for cancer patients and I want to correlate the genes with survival.
>  One option is the survival analysis of the PAM package. However, only the windows EXCEL version offers this option, but the package for R not. Moreover, the EXCEL version breaks down, so that I can see the successfull classification but I can not see which genes are included in the discriminative signature. Unfortunatelly, the authors of PAM do not respond to my questions.
>
>  Questions:
>  1. is there an R version of PAM which I am unaware of?
>  2. is there other pacakge / software I can use to correlate microarray data and patient survival data?

Have you looked at "Semi-Supervised Methods to Predict Patient Survival 
from Gene Expression Data"

         http://dx.doi.org/10.1371/journal.pbio.0020108

???

The R code Bair and Tibs used is in the supplements.

HTH,

Chuck



Charles C. Berry                        (858) 534-2098
                                          Dept of Family/Preventive Medicine
E mailto:cberry at tajo.ucsd.edu	         UC San Diego
http://biostat.ucsd.edu/~cberry/         La Jolla, San Diego 92093-0901