[BioC] Limma :: decideTest question
Lorenzo Bomba
lory.bomb at gmail.com
Thu Oct 14 16:08:12 CEST 2010
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
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