On Thu, May 20, 2010 at 11:57 AM, varpal singh <gilvarpal@gmail.com> wrote:

> Respected Sir,
> Sory sir, am distruing you again, but my all results depend on it.
> I'm sending you two outputs that I got, Just, I would like to know which
> contrast is rigt, in two condition only ??
> *c<-makeContrasts(group2-group1,levels=design) OR **
> c<-makeContrasts(group1-group2,levels=design)
> *Because i get result opposite in both cases, that you can see in these
> two probe below *253416_at, 266294_at
> FIRST*
> library(affy)
> data <- ReadAffy()
>  design<- model.matrix(~0+factor(c(1,1,2,2)))
> colnames(design)<-c("group1", "group2")
>  *c<-makeContrasts(group2-group1,levels=design)*
> eset <- rma(data)
> fit <- lmFit(eset,design)
> fit2 <- contrasts.fit(fit,c)
>  fit2 <- eBayes(fit2)
>  topTable(fit2, coef=1, adjust="fdr", number=10)
>                ID     logFC  AveExpr         t      P.Value
> adj.P.Val         B
> 8516    253416_at  *7.122005* 7.535481  26.57534 2.255100e-05 0.3000238
> 1.4319777
> 21394   266294_at  *5.221736* 7.090044  24.38216 3.100325e-05 0.3000238
> 1.3731773
>
> -------------------------------------------------------------------------------------------
> *
>
> SECOND*
> design<- model.matrix(~0+factor(c(1,1,2,2)))
> colnames(design)<-c("group1", "group2")
> *c<-makeContrasts(group1-group2,levels=design)*
> fit2 <- contrasts.fit(fit,c)
> fit3 <- eBayes(fit2)
> topTable(fit3, coef=1, adjust="fdr", number=10)
>                ID     logFC  AveExpr         t      P.Value
> adj.P.Val         B
> 8516    253416_at *-7.122005* 7.535481 -26.57534 2.255100e-05 0.3000238
> 1.4319777
> 21394   266294_at* -5.221736* 7.090044 -24.38216 3.100325e-05 0.3000238
> 1.3731773
>
>
Hi, Varpal.

They should be opposite, yes.  Otherwise, the results should be identical
and it appears that they are.

Sean

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