I'm making a de analysis using Limma, and I have a lot of samples. I trying to compute the design matrix and then the lmFit(). But when I call lmFit it returns
coefficient not estimable
refering for the last coefficient in the design matrix. There were some NA values for some rows, so before to compute the design matrix i deleted them. This is the code:
delete = rownames(x$samples)[!complete.cases(x$samples)]
x$samples = x$samples[!rownames(x$samples) %in% delete,]
x$counts = x$counts[,!colnames(x$counts) %in% delete]
design <- model.matrix(~0+group+gender+y+age, data=x$samples)
colnames(design) <- gsub("group", "", colnames(design))
v <- voom(x, design)
vfit <- lmFit(v, design)
where x is a DGE object. y is a numeric variable containing almost different values. So when i create the design matrix, it contains a lot of columns because the variable y has a lot of levels. So maybe I should create a new varaible y2 that divide the values in y in some categorie using ifelse() function.