[BioC] multtest and Cox regression

[Benjamin Haibe-Kains]

Hi,

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 ?

Best,

-- 
Benjamin Haibe-Kains
	[http://www.ulb.ac.be/di/map/bhaibeka/]

Machine Learning Group (ULB)
	[http://www.ulb.ac.be/di/mlg/]

MicroArray Unit (IJB)
	[http://www.bordet.be/servmed/array/]