I am using globaltest for survvival association with expression values.
I was interesting in an specific pathway, 00350 which contain a gene  
called TYRP1.
The pathway was not significant but I plot the global test result  
just to see it. There TYRP1 appear red (+ assoc w/ survival) but when  
I check the coxph model, appears to be negative.
If somebody can point out what it is wrog, I would appreciate.
I include the code below and the output. I am working with the last  
BioC version, and the exprSet object is from hgu133a2.

best

mayte

here

tid<-"205694_at"

#Univariate analysis of TYRP1
 >x<-exprs(reset)[tid,];time=pData(reset)[,"SurvTime"];status=pData 
(reset)[,"Death"];
 > coxph(Surv(time,status)~x,data=list(time,status,x))
Call:
coxph(formula = Surv(time, status) ~ x, data = list(time, status,
     x))
       coef exp(coef) se(coef)       z    p
x -0.00549     0.995   0.0613 -0.0896 0.93

Likelihood ratio test=0.01  on 1 df, p=0.928  n= 23

#By globaltest (only of TYRP1)
#This is just to crosscheck.
gt<-globaltest(reset[tid,],"Surv(SurvTime,Death)")
 > gt
Global Test result:
Data: 23 samples with 1 genes; 1 pathway tested
Model: survival
Method: Asymptotic distribution
     Genes Tested Statistic Q Expected Q sd of Q P-value
all     1      1     -1.2185          0       1 0.88848
 >

which agreed with the cox regression


gt.kegg<-globaltest(reset,"Surv 
(SurvTime,Death)",kegg2,method='p',nperm=500)
gt.kegg["00350"]
Global Test result:
Data: 23 samples with 16181 genes; 1 pathway tested
Model: survival
Method: 500 random permutations

       Genes Tested Statistic Q Expected Q sd of Q P-value
00350    92     70    -0.98048   -0.23591 0.95415    0.79

myplot<-geneplot(gt.kegg["00350"],plot=FALSE)
myplot[tid,]
        name Influence Expected SD   z.score colouring
1 205694_at -1.218468        0  1 -1.218468         +

So here TYRP1 is plot as positively associated with survival.


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