[BioC] LIMMA:linear model and contrast.fit

[Gordon Smyth]

This error would occur because you have set the printer-layout information 
in your MAList to show that the arrays have an arrangement of replicate 
spots in a way that does not match the dimensions of your arrays. Type 
MA$printer and you should see a value for ndups greater than one. Or 
alternatively you specified ndups in your call to lmFit().

None of the commands you show could have set ndups. What extra commands 
have you used not given here?

Gordon

At 10:12 PM 20/01/2005, bioconductor-request at stat.math.ethz.ch wrote:
>Date: Thu, 20 Jan 2005 10:32:56 +0100
>From: Sebastian Thieme <Tobar at gmx.de>
>Subject: [BioC] LIMMA:linear model and contrast.fit
>To: Bioconductor at stat.math.ethz.ch
>
>
>Hello !
>
>I try to use LIMMA according to common reference design as descripted in
>the User's guide.
>The data are stored in variable RGraw:
>
>  >QAfile<-dir(pattern="*\\.txt")
>  >RGraw<-read.maimages(QAfile, source="quantarray", wt.fun=wtIgnore.Filter)
>
>The experiment has the following design:
>
>  >targets <- readTargets("experimente.info")
>  > targets
>                  SlideNumber     Name    FileName        Cy3     Cy5
>e78             1               e78     e78.txt         M1      G1
>e73             2               e73     e73.txt         M1      G1
>w21             3               w21     w21.txt         M1      G2
>w18             4               w18     w18.txt         M1      G2
>  >design <- modelMatrix(targets,ref="M1")
>  >design
>                  G1      G2
>e78     1       0
>e73     1       0
>w21             0       1
>w18     0       1
>
>I normalize the following way:
>
>  >MA<-normalizeWithinArray(RGraw,method="loess")
>
>Then I want to make the linear modell like this
>
>  >fit<-lmFit(MA,design=Design
>
>but I get the error message:
>
>Error in unwrapdups(M, ndups = ndups, spacing = spacing) :
>          dim<- : dims [product 0] do not match the length of object [5760]
>
>The following plan is:
>
>  >contrast.matrix <- makeContrasts("G1","G2","G1-M1","G2-M1",levels=design)
>  >fit2 <- contrasts.fit(fit, contrast.matrix)
>  >fit2 <- eBayes(fit2)
>
>I've no clue where the error is. Could anybody give a hint? And are the
>following steps useful?
>
>Thanks!
>
>Sebastian Thieme