[BioC] multtest and Cox regression

Benjamin Haibe-Kains benjamin.haibekains at bordet.be
Sun Apr 17 18:47:53 CEST 2005


I would want to perform a filtering of my genes according to the 
p-values of univariate Cox regression (so, if I have 100 genes, I 
compute 100 Cox regression with only one gene at a time). Because I 
perform multiple statistical test, I would want to use a multiple 
testing procedure to get adjusted p-values.

I have seen that the MTP function from the multtest package does exactly 
what I need. When I used this function with the Cox parameter

r <- MTP(X=data, Y=Surv(time, event), test="coxph.YvsXZ", B=100)

and I look the unadjusted p-values (r at rawp), they do not correspond to 
the univariate p-values returns by the summary of the coxph function 
(p.value <- 1 - pchisq(z^2, df=1) where z is the z-statistic). Actually, 
when I look at the code, the computed statistic is identical but the 
distribution against this statistic is compared is not the same (in the 
MTP function, this function is estimated by bootstrap, it's not the 
chisq). I don't understand this fact.

Can anyone give me further details about that ?


Benjamin Haibe-Kains

Machine Learning Group (ULB)

MicroArray Unit (IJB)

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