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dms100
2012 May 04
0
LIMMA decideTests result zero from contrast matrix
...mall glitch somewhere at my end that i get zero counts for my summary(decideTests). Please find below my code and i would really appreciate any help here at all.
Thanks,
Ekta
## R Script ###
> numGenes <- nrow(eset)
> library(limma)
> samples <- c("Un","Un","DMSO10","DMSO10","DMSO5","DMSO5");
> fl <- as.factor(samples)
> design <- model.matrix(~ 0+ fl)
> colnames(design) <- levels(fl)
> fit <- lmFit(eset, design)
> cont.matrix <- makeContrasts(DMSO10-Un, DMSO5-Un, levels=design)
> fit2 <-...