I tried to help on a post one month ago, but without success.
I continue to have problems analyzing the HumanHT-12 chip, I'm trying to follow this code by @Gordon Smyth.
My biggest problem is to split the groups, how to tell the R what Healthy controls and the patients.
> library(limma) > x <- read.ilmn("GSE74629_non-normalized.txt",expr="SAMPLE ",probeid="ID_REF") Reading file GSE74629_non-normalized.txt ... ... > y <- neqc(x) Note: inferring mean and variance of negative control probe intensities from the detection p-values. > Group <- rep(c("PDAC","Healthy"),c(36,14)) > Group <- factor(Group) > design <- model.matrix(~Group) > keep <- rowSums(y$E>5) >= 14 > y2 <- y[keep,] > fit <- lmFit(y2,design) > fit <- eBayes(fit,trend=TRUE,robust=TRUE) > topTable(fit,coef=2)
Can I use something like
targets <- readTargets ("targets.txt") ? and then say what are the controls and patients:
#Build the design matrix for the linear modelling function f <- factor(targets$Target, levels = unique(targets$Target)) design <- model.matrix(~0 + f) colnames(design) <- levels(f) #Create a contrast matrix contrast.matrix <- makeContrasts("patients-control", levels=design)
Thank you all,