[BioC] FRD : package fdrame vs multtest

[Nicolas Servant]

Hi all,

I would like to compare the two packages "multtest" and "frame" to 
compare the two FDR function.
I test them on the Golub data, and perform the simple LSU (Linear Step 
Procedure) procedure.
The both results are not exactly the same...

##multtest package
test<-mt.teststat(golub,golub.cl, test="t.equalvar")
pval.test <- 2*(pt(-abs(test),36))
resFDR<-mt.rawp2adjp(pval.test, proc=c("BH"))
adjp <- resFDR$adjp[order(resFDR$index),]

##fdrame
fdrame<-fdr.ma(golub,golub.cl,p.method="theoretic",fdr.adj="BH-LSU")

The fdrame package use the Student test, and i verified that the 
fdram$dif data were the same that the mt.teststat$teststat.num data.
Therefore i suppose that the no adjusted pvalues are equally the same.

The first 10 results (pval    fdrame    adjp-multtest):
  
 [1] "0.0170276669459720     0.201688145549621     0.068292673088116"
 [2] "0.255228106990335     0.544842407507294     0.436736373767533"
 [3] "0.913030948999123     0.959693978582492     0.956613126853133"
 [4] "0.786674366368     0.841218391749495     0.879495599776024"
 [5] "0.243146660088367 0.334140455294467     0.425855602715044"
 [6] "0.281983317344268     0.376018736206403     0.466714155158842"
 [7] "0.62418676693191     0.645068479616667     0.769314565346159"
 [8] "0.716299487029608     0.74157426271768     0.83001509112318"
 [9] "0.991113269533743     0.992994429086477     0.995026846116305"
[10] "0.928212225072347     0.943350294841212     0.96310489568757"


If anybody have an idea to explain how can i observe such a difference ...
Is it exactly the same procedures ?

Best regards,

Nicolas Servant

-- 
Nicolas Servant
Equipe Bioinformatique
Institut Curie 
26, rue d'Ulm - 75248 Paris Cedex 05 - FRANCE

Email: Nicolas.Servant at curie.fr
Tel: 01 44 32 42 75