[BioC] Any problem with the design matrix or the contrasts? Thanks

[Federico Lasa]

Both a question and a quick suggestion..

For the first case, should/does

design <- model.matrix(~0+AR +gender +chip, data=targets)
cm<-makeContrasts(ARpos-ARneg, levels=design)

produce the same results you have?

On Fri, Aug 1, 2014 at 10:07 AM, Rao,Xiayu <XRao at mdanderson.org> 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