Hello,

I learned from posts in the forum and analyzed my data using the suggested design and contrasts. It turns out there are no sig genes or few in the end. Could you please help check if the design does not fit the data or the contrasts made are incorrect??

#the research questions are 1) to compare between pos and neg for AR,  and 2) Male.pos vs. Female.pos.

Treat <- factor(paste(targets$gender,targets$AR,sep="."))
chip <- factor(targets$chip)
design <- model.matrix(~0+Treat+chip)
colnames(design)[1:4] <- levels(Treat)
fit <- lmFit(y,design)

cm <- makeContrasts(posVSneg=(F.pos+M.pos-F.neg-M.neg)/2, MposVSFpos=M.pos-F.pos, levels=design)
fit2 <- contrasts.fit(fit,cm)
fit2 <- eBayes(fit2)
topTable(fit2, coef="posVSneg", sort.by="p")           #0 sig genes
topTable(fit2, n=20,coef="MposVSFpos", sort.by="p")             #4 sig genes

targets.txt
sample gender AR          chip
s1            F              pos         1
s2            F              neg        1
s3            M            neg        2
s4            M            pos         2
s5            F              neg        2
s6            M            pos         2
s7            M            pos         2
s8            M            pos         3
s9            M            pos         3
s10         M            pos         3
s11         M            pos         3
s12         F              pos         4
s13         F              pos         4
s14         M            pos         4
s15         M            pos         4
s16         F              pos         5
s17         M            pos         5
s18         M            pos         5
s19         M            neg        6
s20         M            neg        6
s21         F              neg        6
s22         F              pos         6
s23         F              pos         6
s24         F              neg        6
s25         F              pos         6
s26         F              pos         6
s27         F              pos         6
s28         M            neg        6


Thanks,
Xiayu

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