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