Hi, i'm having problems to create a contrast from a manova fit object. The MAANOVA package is doing that perfectly but i can't use it as i'm not using arrays. >> pData: Celltype Patient Group pat1.cell1 Bcell 1 normal pat1.cell2 Tcell 1 normal pat2.cell1 Bcell 2 severe pat2.cell2 Tcell 2 severe pat2.cell1 Bcell 3 mild pat2.cell2 Tcell 3 mild My data.eset matrix looks like that exprs(mydata.eset) exprs: pat1.cell1 pat1.cell2 ..... gene1 0.18 1.2 gene2 0.56 1.5 gene3 0.20 1.3 gene4 0.56 2.2 ... group=c(as.character(unique(phenotype$Group))) patient=c(as.character(unique(phenotype$Patient))) celltype=c(as.character(unique(phenotype$Celltype))) #The function design.list is a custom copded encoded function to easily create the numeric values for the different variables groups = factor(c(design.list(phenotype$Group,group))) celltypes = factor(c(design.list(phenotype$Celltype,celltype))) patients = factor(c(design.list(phenotype$Patient,patient))) >fit<- manova( t(exprs(mydata.eset)) ~ celltypes*groups) >summary.aov(fit) Response GeneA : Df Sum Sq Mean Sq F value Pr(>F) celltypes 1 1429.65 1429.65 403.8082 < 2.2e-16 *** groups 2 6.22 3.11 0.8783 0.418247 celltypes:groups 2 38.91 19.45 5.4948 0.005248 ** Residuals 116 410.69 3.54 This is telling me that a particular gene is differentially expresed betwee, celltypes and groups . Can i see which genes are differentially expressed betwee pariwise groups. For example gene A is differentially expressed between celltypes and groups but i still don't know if it expression changes between normal and mild on one side and severe and mild on the other hand. Normally i would do that by building an anova pairwise design for each celltype: > contrast.matrix <- design.pairs(c("normal", "mild", "severe")) > contrast.matrix normal-mild normal-severe mild-severe normal 1 1 0 mild -1 0 1 severe 0 -1 -1 fit2 <- contrasts.fit(fit, contrast.matrix) That will not work for a manova fit object because of celltype. How can i fix this ?? any idea ??? I though it would usefull to use the MAAANOVA package for that but is there a way to create a madata object from my eset object ?? it might make things easier ? At the end i also have an expression data matrix and it would be extremely useful to create design. thanks