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Question: LIMMA:linear model and contrast.fit
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gravatar for Sebastian Thieme
13.6 years ago by
Sebastian Thieme30 wrote:
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
ADD COMMENTlink modified 13.6 years ago • written 13.6 years ago by Sebastian Thieme30
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gravatar for Gordon Smyth
13.6 years ago by
Gordon Smyth34k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth34k wrote:
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@stat.math.ethz.ch wrote: >Date: Thu, 20 Jan 2005 10:32:56 +0100 >From: Sebastian Thieme <tobar@gmx.de> >Subject: [BioC] LIMMA:linear model and contrast.fit >To: Bioconductor@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
ADD COMMENTlink written 13.6 years ago by Gordon Smyth34k
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gravatar for Sebastian Thieme
13.6 years ago by
Sebastian Thieme30 wrote:
ADD COMMENTlink written 13.6 years ago by Sebastian Thieme30
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