[BioC] globaltest procedure

Goeman, J.J. (MSTAT) J.J.Goeman at lumc.nl
Mon Mar 14 12:06:11 CET 2005

Dear Jeff,

Sorry I'm so late in replying. I missed your mesage. 

Suppose you have an exprSet called ES with phenoData variables "survival", indicating the survival time, "death" indicating whether the patient died (1) or was censored (0), plus maybe some extra phenoData variabeles "A", "B", "C". Your pathways are coded in a list called pathways. Then your input should be:

gt <- globaltest(ES, "survival", pathways, d = "death")

If you want to adjust the analysis for the covariates A, B, C, you say

gt <- globaltest(ES, survival ~ A + B + C, pathways, d = "death")

If you coded things differently, for example you have a variable "censored", which is 1 if the patient was censored, 0 if he or she died, you may use

gt <- globaltest(ES, survival ~ A + B + C, pathways, d = "censored", event = 0)

I hope this solves your problem. 



> -----Original Message-----
> From: zhifu sun [mailto:szf602 at yahoo.com]
> Sent: 09 March 2005 05:01
> To: BioConductor mailing list
> Subject: [BioC] globaltest procedure
> Can somebody share some experience on how to use the
> "globlatest" function in "globaltest" package?
> Specifically I would like to use it to test the
> association between genes in a pathway and survival. I
> also have 6 covariates (phenotype variables, the
> esprSet object already created with these variables)
> for adjustment. After several tries, I could not make
> it work (the documentation for the package does not
> give details on this kind of analysis) and really
> appreciate someone's help.    
> Thank you in advance.
> Jeff Sun

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