Hello, When I use the block variable in the lmFit, data in the MArrayLM have different dimension : > dim(analysis$fit) [1] 6936 3 > dim(analysis$fit$coef) [1] 6936 3 > dim(analysis$fit$genes) [1] 2312 6 Here is the command line I've passed and a description of the data I've used : analysis$fit <- lmFit( msData, design=analysis$effects$Designmatrix , block = msData$block , ndups=msData$printer$ndups, spacing=msData$printer$spacing, weights=NULL ) > dim(msData) [1] 6936 15 > msData$block [1] 1 1 2 3 3 4 4 5 5 6 6 7 7 8 8 > msData$printer$ndups [1] 3 > msData$printer$spacing [1] 1 > analysis$effects$Designmatrix A B C Array1 1 0 0 Array2 -1 0 0 Array3 1 0 0 Array4 1 0 0 Array5 -1 0 0 Array6 0 1 0 Array7 0 -1 0 Array8 0 1 0 Array9 0 -1 0 Array10 0 0 1 Array11 0 0 -1 Array12 0 0 1 Array13 0 0 -1 Array14 0 0 1 Array15 0 0 -1 Am I doing something wrong or it is a problem in the lmFit function? Thanks a lot. Laetitia Marisa.

>Date: Tue, 19 Apr 2005 10:46:51 +0200 >From: Laetitia Marisa <laetitia.marisa@cgm.cnrs-gif.fr> >Subject: [BioC] Limma : Problem with lmFit() and block >To: bioconductor@stat.math.ethz.ch >Message-ID: <4264C57B.8080403@cgm.cnrs-gif.fr> >Content-Type: text/plain; charset=ISO-8859-15; format=flowed > >Hello, > >When I use the block variable in the lmFit, data in the MArrayLM have >different dimension : > > > dim(analysis$fit) >[1] 6936 3 > > > dim(analysis$fit$coef) >[1] 6936 3 > > > dim(analysis$fit$genes) >[1] 2312 6 The problem here is that fit$genes and fit$coef should always have the same number of rows. The problem has occured because you have specified both 'ndups' and 'block' to lmFit() simultaneously, whereas lmFit() can only handle one of these at a time. I will change lmFit() so that it generates an error when ndups>2 and 'block' are set simultaneously. Gordon >Here is the command line I've passed and a description of the data I've >used : > >analysis$fit <- lmFit( msData, design=analysis$effects$Designmatrix , >block = msData$block , ndups=msData$printer$ndups, >spacing=msData$printer$spacing, weights=NULL ) > > > dim(msData) >[1] 6936 15 > > msData$block > [1] 1 1 2 3 3 4 4 5 5 6 6 7 7 8 8 > > msData$printer$ndups >[1] 3 > > msData$printer$spacing >[1] 1 > > > analysis$effects$Designmatrix > A B C >Array1 1 0 0 >Array2 -1 0 0 >Array3 1 0 0 >Array4 1 0 0 >Array5 -1 0 0 >Array6 0 1 0 >Array7 0 -1 0 >Array8 0 1 0 >Array9 0 -1 0 >Array10 0 0 1 >Array11 0 0 -1 >Array12 0 0 1 >Array13 0 0 -1 >Array14 0 0 1 >Array15 0 0 -1 > >Am I doing something wrong or it is a problem in the lmFit function? > >Thanks a lot. > >Laetitia Marisa.