[BioC] Any problem with the design matrix or the contrasts? Thanks
Ryan C. Thompson
rct at thompsonclan.org
Fri Aug 8 23:14:26 CEST 2014
Hi,
You're going to need to address your two scientific questions using
separate fits. This is because your first question (pos vs neg) is
testing a main effect, and you are effectively fitting an interaction
model (one coefficient for each combination of AR & gender). So your
interaction model is correct for testing the second question, which is
testing one factor within only a single level of the other. But for
testing the main effect, you'll need to fit an additive model using the
formula suggested by Federico. Furthermore, the test for a main effect
may not be valid in the presence of an interaction effect, so you should
test for that too using the interaction model, and then look closely at
the data before trusting probe sets that are significant for both the
main effect and interaction effect. The interaction contrast using your
design would be ((F.pos-M.pos)-(F.neg-M.neg)).
-Ryan
On 08/01/2014 08:07 AM, Rao,Xiayu 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
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor
mailing list