Hi all, I would like to ask a question about the function decideTest: I'm analysing microarray data and I'm using a the following commands to get the differentially express genes: #RDE is a MAlist object target<-read.table(file="TargetALL.txt", header=TRUE) TS <- factor(target$Diet, levels=c("CTR0","CTR","TRT")) design <- model.matrix(~0+TS) colnames(design) <- c("CTR0","CTR","TRT") fit3_1 <- lmFit(RDE,design,weights=RDE$weights) cont.matrix <- makeContrasts(CTR0vsCTR = CTR0-CTR, CTR0vsTRT= CTR0-TRT, CTRvsTRT= CTR-TRT,levels=design) fit3_1c <- contrasts.fit(fit3_1, cont.matrix) fit3 <- eBayes(fit3_1c) TableDEGfit3T <- topTable(fit3, adjust="BH", number= 29767) # follow the "TargetALL.txt" file that I use to create the design matrix FileName Diet S1M CTR0 S2 CTR0 S3 CTR0 S4 CTR0 S6 CTR0 S10M CTR S11 CTR S12 CTR S13 CTR S14 CTR S15 CTR S17rt TRT S18 TRT S19 TRT S20 TRT S21 TRT S22 TRT #after I make a SEPARATE decide test I got the number of gene in common between CTR0vsCTR and CTR0vsTRT contrast like in the venn #diagramm following results <- decideTests(fit3,p.value=0.01) #Venn Diagrams jpeg("Venndigramsnocov.jpg") vennDiagram(results) dev.off() -------------- next part -------------- after that I tried to do separate analysis of the two control using this commands #CONTRAST: CTR0vsCTR target<-read.table(file="TargetALL.txt", header=TRUE) TS <-factor(target$Diet,levels=c("CTR0","CTR")) design <- model.matrix(~-1+TS) colnames(design) <- c("CTR0","CTR") fit4_1 <- lmFit(RDEctr0ctr,design,weights=RDEctr0ctr$weights) cont.matrix <- makeContrasts(CTR0vsCTR= CTR0-CTR,levels=design) fit4_1c <- contrasts.fit(fit4_1, cont.matrix) fit4 <- eBayes(fit4_1c) TableDEGfit4T <- topTable(fit4, adjust="BH", number= 29767) #CONTRAST: CTR0vsTRT target<-read.table(file="TargetALL.txt", header=TRUE) TS <-factor(target$Diet,levels=c("CTR0","TRT")) design <- model.matrix(~-1+TS) colnames(design) <- c("CTR0","TRT") fit5_1 <- lmFit(RDEctr0ctr,design,weights=RDEctr0ctr$weights) cont.matrix <- makeContrasts(CTR0vsTRT= CTR0-TRT,levels=design) fit5_1c <- contrasts.fit(fit5_1, cont.matrix) fit5 <- eBayes(fit5_1c) TableDEGfit5T <- topTable(fit5, adjust="BH", number= 29767) and than I tried to figured out what are the gene in common that I've suppose to be the same number of the vennDiagram: 6472 genes in common p001_4<-which(TableDEGfit4T$adj.P.Val <= 0.01) p001_5<-which(TableDEGfit5T$adj.P.Val <= 0.01) Descr4_001<-TableDEGfit4T$Description[p001_4] Descr5_001<-TableDEGfit5T$Description[p001_5] com <- match(Descr4_001, Descr5_001) length(which(com != "NA")) after This I got this number 4176 instead 6472 I cannot understand because in the decideTest the contrast are take separately ......... Thanks in advance for the help! Lorenzo Bomba