[BioC] Dose response linear correlation using Limma

Christian De Santis christian.desantis at stir.ac.uk
Thu Jul 10 16:20:13 CEST 2014


Dear all,

i tried to extract genes that are linearly correlated to a dose response in a dietary experiment using the following script. 

dm <- model.matrix(~ DHA, data=targets)
fit <- lmFit(MA.list,dm)
fit2 <- eBayes(fit)
table <- topTable(fit2,coef=2, adjust.method="none", number = 10000, p.value = 0.05)

the first time i did it i had in the output two columns with the intercept and the slope but i did it again and now I do not get them anymore. I can't figure out why as i dont think i have changed anything, but obviously i must have. Just to confirm however, is the slope equivalent to the fit2$coefficients values?

Thanks,
Christian 
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