Question: Any problem with the design matrix or the contrasts? Thanks

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Rao,Xiayu •

**530**wrote: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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modified 4.5 years ago
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Ryan C. Thompson ♦

**7.2k**• written 4.6 years ago by Rao,Xiayu •**530**