Hi everyone,

I am new to microarray data analysis. Please evaluate the following code for  block analysis in Limma and let me know about whether this code is appropriate??.

library(limma)
eset<-read.table("RMANormData_apap.txt")
design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2,3,3,3,4,4,4,5,5,5,6,6,6)))
colnames(design) <- c("control3", "control24", "low3","high3","low24","high24")
contrast.matrix <- makeContrasts(high3-control3,high24-control24,low3-control3,low24-control24 , levels=design)
sample<-read.table("sample.txt",sep="\t",as.is=T,h=T)
corfit<-duplicateCorrelation(eset,design,ndups=1,block=sample[,3])
fit<-lmFit(eset,design,block=sample[,3],cor=corfit$consensus)
fit2<-contrasts.fit(fit,contrast.matrix)
fit2<-eBayes(fit2)
topTable(fit2, coef=1, adjust="fdr", sort.by="B", number=10)
results <- decideTests(fit2,adjust.method="BH",method="separate",lfc=1, p.value=0.05);

The input table RMANormData_apap.txt containing the expression values of the genes includes the following columns:
c_3_1  c_3_2  c_3_3  c_24_1  c_24_2  c_24_3   t_1l_3h_1    t_1l_3h_2   t_1l_3h_3  t_5l_3h_1    t_5l_3h_2  t_5l_3h_3  t_1l_24h_1  t_1l_24h_2  t_1l_24h_3 t_5l_24h_1    t_5l_24h_2  t_5l_24h_3

the input file sample.txt contains the following information:
Sample Group      Block
c_3_1control3        1
c_3_2control3        2
c_3_3control3        3
c_24_1control24        1
c_24_2control24        2
c_24_3control24        3
t_1l_3h_1 low3                1
t_1l_3h_2 low3           2
t_1l_3h_3 low3                3
t_5l_3h_1 high3                1
t_5l_3h_2high3                2
t_5l_3h_3high3                3
t_1l_24h_1low24         1
t_1l_24h_2low24         2
t_1l_24h_3low24         3
t_5l_24h_1high24         1
t_5l_24h_2high24         2
t_5l_24h_3high24         3since the experiment is performed using  3 rats block factor in included.

Regards,
Sri
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