Hi i try to make an analysis of a microarray with the limma package, i'm new and inexperiment in this my problem is just before doing the lmFit() i have to make a model.matrix, but i don't understant very well the process to do that. i describe my experiment : i have 6 samples, three of theme are biological replicate for each conditions : without iron with iron : -a -d -b -e -c -f and i want to see the expressed genes (over or under) in the second conditions, the first are the reference how i must write my model.matrix to continue my analysis please ? i try this one, but it seems not working : design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2))) this is my sessionInfo : > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8 [5] LC_MONETARY=C LC_MESSAGES=fr_FR.utf8 [7] LC_PAPER=fr_FR.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.26.1 Biobase_2.8.0 limma_3.4.5 loaded via a namespace (and not attached): [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.1 > -- MOZAR Michaël Master Bioinformatique Université de Nantes 0688715937 [[alternative HTML version deleted]]

Hi Michael, Is this a single-channel experiment with 6 arrays and two RNA sources? If yes, then Section 8.5 of the Users Guide has a good example for computing the design matrix. Chapter 7 is also useful. http://bioconductor.org/help/bioc-views/2.8/bioc/html/limma.html Valerie On 11/12/2010 05:13 AM, Michael MOZAR wrote: > Hi > i try to make an analysis of a microarray with the limma package, i'm new > and inexperiment in this > my problem is just before doing the lmFit() i have to make a model.matrix, > but i don't understant very well the process to do that. > i describe my experiment : > > i have 6 samples, three of theme are biological replicate for each > conditions : > without iron with iron : > -a -d > -b -e > -c -f > > and i want to see the expressed genes (over or under) in the second > conditions, the first are the reference > how i must write my model.matrix to continue my analysis please ? > > i try this one, but it seems not working : > > design <- model.matrix(~ -1+factor(c(1,1,1,2,2,2))) > > this is my sessionInfo : > > >> sessionInfo() >> > R version 2.11.1 (2010-05-31) > x86_64-pc-linux-gnu > > locale: > [1] LC_CTYPE=fr_FR.utf8 LC_NUMERIC=C > [3] LC_TIME=fr_FR.utf8 LC_COLLATE=fr_FR.utf8 > [5] LC_MONETARY=C LC_MESSAGES=fr_FR.utf8 > [7] LC_PAPER=fr_FR.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=fr_FR.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.26.1 Biobase_2.8.0 limma_3.4.5 > > loaded via a namespace (and not attached): > [1] affyio_1.16.0 preprocessCore_1.10.0 tools_2.11.1 > >> > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]