I am trying to do a differential methylation analysis of probes in R using "days to death" as my clinical factor. I have values ranging from 9 to 3258 days and need to make contrasts between these values, but there are too many values to do this manually. Is there a automatic way to contrast a wide range of continuous values? If not, can I specify ranges (i.e. 0-500, 501-1000 days, etc.) and input this into the "makecontrasts" function (not sure how to go about doing this). Below is the code I am using.
outcome <- factor(targets$days_to_death) design <- model.matrix(~0+outcome, data=targets) colnames(design) <- c(levels(outcome)) fit <- lmFit(MVals_d2d, design) contMatrix <- makeContrasts(**?????**, levels=design) fit2 <- contrasts.fit(fit, contMatrix) fit2 <- eBayes(fit2) summary(decideTests(fit2)) ann450kSub <- ann450k[match(rownames(mVals),ann450k$Name), c(1:4,12:19,24:ncol(ann450k))] DMPs <- topTable(fit2, coef=NULL, adjust.method="fdr", p.value=0.05, genelist=ann450kSub)
Thank you in advance.